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  • A61K31/33—Heterocyclic compounds
  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
  • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
  • A61K31/519—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with heterocyclic rings
  • A61K31/52—Purines, e.g. adenine
  • A61K31/522—Purines, e.g. adenine having oxo groups directly attached to the heterocyclic ring, e.g. hypoxanthine, guanine, acyclovir
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  • A61K31/7088—Compounds having three or more nucleosides or nucleotides
  • A61K31/7105—Natural ribonucleic acids, i.e. containing only riboses attached to adenine, guanine, cytosine or uracil and having 3'-5' phosphodiester links
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  • A61K31/713—Double-stranded nucleic acids or oligonucleotides
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  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K39/395—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum
  • A61K39/42—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum viral
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
  • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
  • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
  • A61K47/54—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound
  • A61K47/549—Sugars, nucleosides, nucleotides or nucleic acids
• • A—HUMAN NECESSITIES
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  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
  • A61K48/005—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy characterised by an aspect of the 'active' part of the composition delivered, i.e. the nucleic acid delivered
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
  • A61P31/12—Antivirals
  • A61P31/20—Antivirals for DNA viruses
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
  • C07K16/08—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from viruses
  • C07K16/081—DNA viruses
  • C07K16/082—Hepadnaviridae (F), e.g. hepatitis B virus
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
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  • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
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  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K2039/54—Medicinal preparations containing antigens or antibodies characterised by the route of administration
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K2039/545—Medicinal preparations containing antigens or antibodies characterised by the dose, timing or administration schedule
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K2300/00—Mixtures or combinations of active ingredients, wherein at least one active ingredient is fully defined in groups A61K31/00 - A61K41/00
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  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
  • C07K2317/24—Immunoglobulins specific features characterized by taxonomic origin containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
• • C—CHEMISTRY; METALLURGY
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  • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
  • C07K2317/52—Constant or Fc region; Isotype
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  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
  • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
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  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin

Definitions

• the lipid envelope includes the hepatitis B surface antigen (HBsAg), which refers to three separate proteins, S-HBsAg (small antigen), M-HBsAg (middle antigen), and L-HBsAg (large antigen) that are encoded by the same open reading frame but utilize distinct start codons.
• HBsAg is the antigen present in currently available hepatitis B vaccines.
• HBV also encodes the protein HBx, which inhibits tumor suppressor p53, promotes cell cycle progression, and increases production of reactive oxygen species.
• HBV In addition to producing virions, HBV also causes production of subviral particles (SVPs), which include the lipid envelope of an HBV virion, but are not replication competent and typically lack the nucleocapsid. SVPs can be produced up to 3-4 log in excess over replication competent virions. High levels of HBsAg preset on the SVPs can exhaust HBsAg- specific T-cell response, which is likely an important factor contributing to the inability of the immune system to clear HBV infection during chronic hepatitis B ( Chisari, F.Y., et al., Pathologie Biologie 58:258-66 (2010 )).
• SVPs subviral particles
• the natural evolution of CHB infection includes four consecutive phases: (1) early 'immunotolerant' phase, which is associated with high levels of virus replication and minimal liver inflammation; (2) immune reactive phase, which is associated with significant hepatic inflammation and elevated serum aminotransferases; with some patients progressing to (3) 'non-replicative' or 'inactive' phase, which is associated with: seroconversion to anti-HBe; an undetectable or low level of viremia (below 2000 IU/ml by PCR-based assays); and resolution of hepatic inflammation; and for some individuals, (4) reactivation of the virus.
• HBeAg-negative chronic hepatitis B Reactivation of HBV infection can be associated with the emergence of specific viral mutations that prevent the production of HBeAg but do not hamper virus replication, which is known as HBeAg-negative chronic hepatitis B.
• HBeAg-negative chronic hepatitis B (also known as anti-HBe-positive or precore mutant hepatitis) is characterized by fluctuating serum HBV DNA and serum aminotransferases (ALT and AST) levels, and progressive liver disease.
• HBV HBV virus
• Clinically important short-term goals include: achieving HBeAg-seroconversion, normalizing serum ALT and AST, resolving liver inflammation, and preventing hepatic decompensation.
• An ultimate long-term goal of HBV treatment is to achieve durable immune response to prevent development of cirrhosis and liver cancer, and therefore prolong survival.
• Currently available HBV treatments do not completely clear the virus due to persistence of cccHBV DNA in the nuclei of infected hepatocytes.
• treatment-induced clearance of serum HBsAg is a marker of termination of chronic HBV infection and has been associated with the best long-term outcome.
• HBV polymerase inhibitors are effective in reducing viral production but have little to no effect in rapidly reducing HBsAg or can slowly reduce HBsAg with long term treatment in a limited number of patients (as is the case with tenofovir disoproxil fumarate).
• Interferon-based immunotherapy can achieve a reduction of both viral production and early removal of HBsAg from the blood, but only in a small percentage of treated subjects.
• HBsAg The generally accepted role of HBsAg in the blood is to sequester anti-HBsAg antibodies and allow infectious viral particles to escape immune detection, which is likely one of the reasons why HBV infection remains a chronic condition.
• HBsAg, HBeAg, and HBcAg all have immuno-inhibitory properties and the persistence of these viral proteins in the blood of patients following the administration of any of the currently available treatments for HBV likely has a significant impact in preventing patients from achieving immunological control of their HBV infection.
• a “(poly)peptide” comprises a single chain of amino acid monomers linked by peptide bonds as explained above.
• a “protein”, as used herein, comprises one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 (poly)peptides, i.e., one or more chains of amino acid monomers linked by peptide bonds as explained above.
• a protein according to the present disclosure comprises 1, 2, 3, or 4 polypeptides.
• the terms “cell,” “cell line,” and “cell culture” are used interchangeably and all such designations include progeny.
• the words “transformants” and “transformed cells” include the primary subject cell and cultures derived therefrom without regard for the number of transfers. It is also understood that all progeny may not be precisely identical in DNA content, due to deliberate or inadvertent mutations. Variant progeny that have the same function or biological activity as screened for in the originally transformed cell are included. Where distinct designations are intended, it will be clear from the context.
• sequence variant refers to any sequence having one or more alterations in comparison to a reference sequence, whereby a reference sequence is any of the sequences listed in the sequence listing, i . e ., SEQ ID NO:1 to SEQ ID NO: 104.
• sequence variant includes nucleotide sequence variants and amino acid sequence variants.
• the reference sequence is also a nucleotide sequence, whereas for a sequence variant in the context of an amino acid sequence, the reference sequence is also an amino acid sequence.
• the substitutions are conservative amino acid substitutions, in which the substituted amino acid has similar structural or chemical properties with the corresponding amino acid in the reference sequence.
• conservative amino acid substitutions involve substitution of one aliphatic or hydrophobic amino acids, e.g., alanine, valine, leucine, and isoleucine, with another; substitution of one hydoxyl-containing amino acid, e.g., serine and threonine, with another; substitution of one acidic residue, e . g ., glutamic acid or aspartic acid, with another; replacement of one amide-containing residue, e .
• nucleic acid sequence or an amino acid sequence "derived from” a designated nucleic acid, peptide, polypeptide, or protein refers to the origin of the nucleic acid, peptide, polypeptide, or protein.
• nucleic acid sequence or amino acid sequence which is derived from a particular sequence has an amino acid sequence that is essentially identical to that sequence or a portion thereof, from which it is derived, whereby "essentially identical” includes sequence variants as defined above.
• nucleic acid sequence or amino acid sequence which is derived from a particular peptide or protein is derived from the corresponding domain in the particular peptide or protein. Thereby, "corresponding" refers in particular to the same functionality.
• expression refers to any step involved in the production of the polypeptide, including transcription, post-transcriptional modification, translation, post-translational modification, secretion, or the like.
• an agent that reduces HBV antigenic load refers to any agent that results in a reduction in the amount of an HBV antigen that can be isolated from or detected in a first cell or group of cells that has or have been treated with the agent, as compared to a second cell or group of cells substantially identical to the first cell or group of cells but which has or have not been so treated (control cells).
• an agent that reduces HBV antigenic load is an RNAi agent (e.g., an siRNA).
• Antigenic load can be measured by methods known in the art.
• "HBV antigenic load” as used herein is determined by measuring by the amount of antigen ( e . g ., HBsAg) using ELISA.
• the present disclosure provides combination therapy to treat HBV, which includes an anti-HBV antibody.
• the anti-HBV antibody or an antigen binding fragment thereof binds to the antigenic loop region of HBsAg and neutralizes infection with hepatitis B virus.
• the term “antibody” encompasses various forms of antibodies including, without being limited to, whole antibodies; antibody fragments, antigen binding fragments, human antibodies, chimeric antibodies, humanized antibodies; recombinant antibodies, and genetically engineered antibodies (variant or mutant antibodies) as long as the characteristic properties of the antibody are retained.
• the antibodies are human antibodies and/or monoclonal antibodies.
• the antibodies are human monoclonal antibodies.
• the antibodies are recombinant human monoclonal antibodies.
• the terms "antigen binding fragment,” “fragment,” and “antibody fragment” are used interchangeably to refer to any fragment of an antibody of the combination therapy that retains the antigen-binding activity of the antibody.
• neutralizing antibody is one that can neutralize, i.e., prevent, inhibit, reduce, impede, or interfere with, the ability of a pathogen to initiate and/or perpetuate an infection in a host.
• neutralizing antibody and “an antibody that neutralizes” or “antibodies that neutralize” are used interchangeably herein. These antibodies can be used alone, or in combination, as prophylactic or therapeutic agents upon appropriate formulation, in association with active vaccination, as a diagnostic tool, or as a production tool as described herein.
• human monoclonal antibodies are also available for the preparation of human monoclonal antibodies ( Cole, et al., Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, p. 77 (1985 ); Boerner, P., et al., Immunol. 147:86-95 (1991 )).
• human monoclonal antibodies are prepared by using improved EBY-B cell immortalization as described in Traggiai, E., et al. (Nat Med. 10(8):871-5 (2004 )).
• the term "human antibody” as used herein also comprises such antibodies which are modified, e . g ., in the variable region, to generate properties as described herein.
• Antibodies of the combination therapy can be of any isotype (e . g ., IgA, IgG, IgM, i.e., a ⁇ , ⁇ , or ⁇ heavy chain), but in certain particular embodiments, the antibodies are IgG. Within the IgG isotype, antibodies may be IgG1, IgG2, IgG3, or IgG4 subclass. In particular embodiments, the antibodies are IgG1. Antibodies of the combination therapy may have a ⁇ or a ⁇ light chain.
• variable region denotes the portion of an antibody light chain (LC) or heavy chain (HC) (typically around the 105-120 amino-terminal amino acids of a mature antibody heavy chain or light chain) that comprises complementarity determining regions ("CDRs") and framework regions ("FRs"), and that is involved directly in binding the antibody to the antigen.
• CDRs complementarity determining regions
• FRs framework regions
• V H and V L regions generally comprise six CDRs (CDRH1, CDRH2, CDRH3; CDRL1, CDRL2, CDRL3).
• Immunoglobulin sequences can be aligned to a numbering scheme (e.g., Kabat, EU, International Immunogenetics Information System (IMGT) and Aho), which can allow equivalent residue positions to be annotated and for different molecules to be compared using Antigen receptor Numbering And Receptor Classification (ANARCI) software tool ( Bioinformatics 15:298-300 (2016 )).
• a numbering scheme e.g., Kabat, EU, International Immunogenetics Information System (IMGT) and Aho
• ANARCI Antigen receptor Numbering And Receptor Classification
• antibody or “antibody of the combination therapy” includes all categories of antibodies, namely, antigen binding fragment(s), antibody fragment(s), variant(s), and derivative(s) of antibodies.
• Antibodies and antigen binding fragments of the present disclosure may, in embodiments, be multispecific (e . g ., bispecific, trispecific, tetraspecific, or the like), and may be provided in any multispecific format, as disclosed herein.
• an antibody or antigen-binding fragment of the present disclosure is a multispecific antibody, such as a bispecific or trispecific antibody. Formats for bispecific antibodies are disclosed in, for example, Spiess, et al. (Mol. Immunol.
• bispecific formats and methods of making the same include, for example, Bispecific T cell Engagers (BiTEs), DARTs, Knobs-Into-Holes (KIH) assemblies, scFv-CH3-KIH assemblies, KIH Common Light-Chain antibodies, TandAbs, Triple Bodies, TriBi Minibodies, Fab-scFv, scFv-CH-CL-scFv, F(ab')2-scFv2, tetravalent HCabs, Intrabodies, CrossMabs, Dual Action Fabs (DAFs) (two-in-one or four-in-one), DutaMabs, DT-IgG, Charge Pairs, Fab-arm Exchange, SEEDbodies, Triomabs, LUZ-Y assemblies, Fcabs, ⁇ -bodies, orthogonal Fabs, DVD-IgG
• the term "vaccine” as used herein is typically understood to be a prophylactic or therapeutic material providing at least one antigen or immunogen.
• the antigen or immunogen may be derived from any material that is suitable for vaccination.
• the antigen or immunogen may be derived from a pathogen, such as from bacteria or virus particles, etc., or from a tumor or cancerous tissue.
• the antigen or immunogen stimulates the body's adaptive immune system to provide an adaptive immune response.
• an "antigen” or an “immunogen” refers typically to a substance which may be recognized by the immune system ( e .
• Doses are often expressed in relation to bodyweight.
• a dose which is expressed as [g, mg, or other unit]/kg (or g, mg, etc.) usually refers to [g, mg, or other unit] "per kg (or g, mg, etc. ) bodyweight", even if the term “bodyweight” is not explicitly mentioned.
• Hepatitis B virus used interchangeably with the term “HBV” refers to the well-known non-cytopathic, liver-tropic DNA virus belonging to the Hepadnaviridae family.
• the HBV genome is partially double-stranded, circular DNA with four overlapping reading frames (that may be referred to herein as "genes,” “open reading frames,” or “transcripts”) : C, X, P, and S.
• the core protein is coded for by gene C (HBcAg).
• Hepatitis B e antigen (HBeAg) is produced by proteolytic processing of the pre-core (pre-C) protein.
• the DNA polymerase is encoded by gene P.
• Gene S is the gene that codes for the surface antigens (HBsAg).
• the HBsAg gene is one long open reading frame which contains three in frame "start" (ATG) codons resulting in polypeptides of three different sizes called large, middle, and small S antigens, pre-S1 + pre-S2 + S, pre-S2 + S, or S.
• AGT frame "start"
• Surface antigens in addition to decorating the envelope of HBV are also part of subviral particles, which are produced at large excess as compared to virion particles, and play a role in immune tolerance and in sequestering anti-HBsAg antibodies, thereby allowing for infectious particles to escape immune detection.
• HBV non-structural protein coded for by gene X
• a to H Eight genotypes of HBV, designated A to H, have been determined, and two additional genotypes I and J have been proposed, each having a distinct geographical distribution.
• the term "HBV" includes any of the genotypes of HBV (A to J).
• the complete coding sequence of the reference sequence of the HBV genome may be found in for example, GenBank Accession Nos. GI:21326584 and GI:3582357.
• HBV Hepatitis B Virus Strain Data
• the International Repository for Hepatitis B Virus Strain Data can be accessed at http://www.hpa-bioinformatics.org.uk/HepSEQ/main.php.
• the term "HBV,” as used herein, also refers to naturally occurring DNA sequence variations of the HBV genome, i . e ., genotypes A-J and variants thereof.
• Dicer a ribonuclease-III-like enzyme, processes the dsRNA into 19-23 base pair short interfering RNAs (siRNAs) with characteristic two base 3' overhangs ( Bernstein, et al., Nature 409:363 (2001 )).
• siRNAs are then incorporated into an RNA-induced silencing complex (RISC) where one or more helicases unwind the siRNA duplex, enabling the complementary antisense strand to guide target recognition ( Nykanen, et al., Cell 107:309 (2001 )).
• RISC RNA-induced silencing complex
• the degree of inhibition can be measured, by example, as the difference between the degree of mRNA expression in a control cell minus the degree of mRNA expression in a treated cell.
• the degree of inhibition can be given in terms of a reduction of a parameter that is functionally linked to HBV gene expression, e . g ., the amount of protein encoded by an HBV gene, or the number of cells displaying a certain phenotype, e . g ., an HBV infection phenotype such as HBV infection, HBV protein expression (such as hepatitis B surface antigen, HBsAg), or changes in cellular gene expression reflecting HBV gene expression ( e . g ., Smc5/6 expression and localization).
• the degree of inhibition may also be measured using a cell engineered to express a reporter gene reflecting HBV RNA expression.
• HBV gene silencing can be determined in any cell expressing the HBV gene, e.g., an HBV-infected cell or a cell engineered to express the HBV gene, and by any appropriate assay.
• the level of HBV RNA that is expressed by a cell or group of cells, or the level of circulating HBV RNA may be determined using any method known in the art for assessing mRNA expression, such as the rtPCR method provided in Example 2 of International Application Publication No. WO 2016/077321A1 and U.S. Patent Application No. US2017/0349900A1 .
• the level of expression of an HBV gene e.g., total HBV RNA, an HBV transcript, e.g., HBV 3.5 kb transcript
• the level of expression of an HBV gene is determined by detecting a transcribed polynucleotide, or portion thereof, e.g., RNA of the HBV gene.
• target sequence refers to a contiguous portion of the nucleotide sequence of an mRNA molecule formed during the transcription of an HBV gene, including mRNA that is a product of RNA processing of a primary transcription product.
• the target portion of the sequence will be at least long enough to serve as a substrate for RNAi-directed cleavage at or near that portion.
• the target sequence will generally be from 9-36 nucleotides in length, e.g., 15-30 nucleotides in length, including all sub-ranges there between.
• the target sequence can be from 15-30 nucleotides, 15-26 nucleotides, 15-23 nucleotides, 15-22 nucleotides, 15-21 nucleotides, 15- 20 nucleotides, 15-19 nucleotides, 15-18 nucleotides, 15-17 nucleotides, 18-30 nucleotides, 18-26 nucleotides, 18-23 nucleotides, 18-22 nucleotides, 18-21 nucleotides, 18-20 nucleotides, 19-30 nucleotides, 19-26 nucleotides, 19-23 nucleotides, 19-22 nucleotides, 19- 21 nucleotides, 19-20 nucleotides, 20-30 nucleotides, 20-26 nucleotides, 20-25 nucleotides, 20- 24 nucleotides,20-23 nucleotides, 20-22 nucleotides, 20-21 nucleotides, 21-30 nucleotides,
• strand comprising a sequence refers to an oligonucleotide comprising a chain of nucleotides that is described by the sequence referred to using the standard nucleotide nomenclature.
• the term "complementary,” when used to describe a first nucleotide sequence in relation to a second nucleotide sequence, refers to the ability of an oligonucleotide or polynucleotide comprising the first nucleotide sequence to hybridize and form a duplex structure under certain conditions with an oligonucleotide or polynucleotide comprising the second nucleotide sequence, as will be understood by the skilled person.
• Such conditions can, for example, be stringent conditions, where stringent conditions can include: 400 mM NaCl, 40 mM PIPES pH 6.4, 1 mM EDTA, 50°C or 70°C for 12-16 hours followed by washing.
• first sequence is referred to as “substantially complementary” with respect to a second sequence herein
• the two sequences can be fully complementary, or they can form one or more, but generally not more than 5, 4, 3 or 2 mismatched base pairs upon hybridization for a duplex up to 30 base pairs, while retaining the ability to hybridize under the conditions most relevant to their ultimate application, e . g ., inhibition of gene expression via a RISC pathway.
• two oligonucleotides are designed to form, upon hybridization, one or more single stranded overhangs, such overhangs shall not be regarded as mismatches with regard to the determination of complementarity.
• an siRNA comprising one oligonucleotide 21 nucleotides in length, and another oligonucleotide 23 nucleotides in length, wherein the longer oligonucleotide comprises a sequence of 21 nucleotides that is fully complementary to the shorter oligonucleotide, can yet be referred to as "fully complementary" for the purposes described herein.
• a polynucleotide that is "substantially complementary" to at least part of a messenger RNA (mRNA) refers to a polynucleotide that is substantially complementary to a contiguous portion of the mRNA of interest (e . g ., an mRNA encoding an HBV protein).
• mRNA messenger RNA
• a polynucleotide is complementary to at least a part of an HBV mRNA if the sequence is substantially complementary to a non-interrupted portion of the HBV mRNA.
• the RNAi agent comprises an siRNA.
• siRNA refers to an RNAi that includes an RNA molecule or complex of molecules having a hybridized duplex region that comprises two anti-parallel and substantially complementary nucleic acid strands, which will be referred to as having "sense” and “antisense” orientations with respect to a target RNA.
• the duplex region can be of any length that permits specific degradation of a desired target RNA through a RISC pathway, but will typically range from 9 to 36 base pairs in length, e.g., 15-30 base pairs in length.
• the duplex can be any length in this range, for example, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, or 36 and any sub-range there between, including, but not limited to 15-30 base pairs, 15-26 base pairs, 15-23 base pairs, 15-22 base pairs, 15-21 base pairs, 15-20 base pairs, 15-19 base pairs, 15-18 base pairs, 15-17 base pairs, 18-30 base pairs, 18-26 base pairs, 18-23 base pairs, 18-22 base pairs, 18-21 base pairs, 18-20 base pairs, 19-30 base pairs, 19-26 base pairs, 19-23 base pairs, 19-22 base pairs, 19-21 base pairs, 19-20 base pairs, 20-30 base pairs, 20-26 base pairs, 20-25 base pairs, 20-24 base pairs, 20-23 base pairs, 20-22 base pairs, 20-21 base pairs, 21-30 base pairs, 21-26 base pairs, 21-25 base pairs, 21-24 base pairs, 21-23 base pairs, and 21-22
• One strand of the duplex region of an siRNA comprises a sequence that is substantially complementary to a region of a target RNA.
• the two strands forming the duplex structure can be from a single RNA molecule having at least one self-complementary region, or can be formed from two or more separate RNA molecules.
• the duplex region is formed from two strands of a single molecule, the molecule can have a duplex region separated by a single stranded chain of nucleotides (herein referred to as a "hairpin loop") between the 3'-end of one strand and the 5'-end of the respective other strand forming the duplex structure.
• the hairpin loop can comprise at least one unpaired nucleotide; in some embodiments the hairpin loop can comprise at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 20, at least 23 or more unpaired nucleotides.
• the two substantially complementary strands of an siRNA are comprised by separate RNA molecules, those molecules need not, but can be covalently connected.
• the connecting structure is referred to as a "linker.”
• antisense strand or "guide strand” refers to the strand of an RNAi agent, e.g., an siRNA, which includes a region that is substantially complementary to a target sequence.
• region of complementarity refers to the region on the antisense strand that is substantially complementary to a sequence, for example a target sequence, as defined herein. Where the region of complementarity is not fully complementary to the target sequence, the mismatches can be in the internal or terminal regions of the molecule.
• the most tolerated mismatches are in the terminal regions, e.g ., within 5, 4, 3, or 2 nucleotides of the 5' and/or 3' terminus.
• RNA molecule or "ribonucleic acid molecule” encompasses not only RNA molecules as expressed or found in nature, but also analogs and derivatives of RNA comprising one or more ribonucleotide/ribonucleoside analogs or derivatives as described herein or as known in the art.
• a "ribonucleoside” includes a nucleoside base and a ribose sugar
• a “ribonucleotide” is a ribonucleoside with one, two or three phosphate moieties.
• the terms “ribonucleoside” and “ribonucleotide” can be considered to be equivalent as used herein.
• RNA can be modified in the nucleobase structure or in the ribose-phosphate backbone structure, e.g ., as described in greater detail below.
• siRNA molecules comprising ribonucleoside analogs or derivatives retain the ability to form a duplex.
• an RNA molecule can also include at least one modified ribonucleoside including but not limited to a 2'-O-methyl modified nucleoside, a nucleoside comprising a 5' phosphorothioate group, a terminal nucleoside linked to a cholesteryl derivative or dodecanoic acid bisdecylamide group, a locked nucleoside, an abasic nucleoside, a 2'-deoxy-2'-fluoro modified nucleoside, a 2'-amino-modified nucleoside, 2'-alkyl-modified nucleoside, morpholino nucleoside, a phosphoramidate, or a non-natural base comprising nucleoside, or any combination thereof.
• a 2'-O-methyl modified nucleoside a nucleoside comprising a 5' phosphorothioate group, a terminal nucleoside linked to a cholesteryl derivative or dodecanoic acid bisde
• an RNA molecule can comprise at least two modified ribonucleosides, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, or more, up to the entire length of the siRNA molecule.
• the modifications need not be the same for each of such a plurality of modified ribonucleosides in an RNA molecule.
• modified RNAs contemplated for use in methods and compositions described herein are peptide nucleic acids (PNAs) that have the ability to form the required duplex structure and that permit or mediate the specific degradation of a target RNA via a RISC pathway.
• PNAs peptide nucleic acids
• nucleotide overhang refers to at least one unpaired nucleotide that protrudes from the duplex structure of an RNAi agent, e . g ., an siRNA.
• an siRNA can comprise an overhang of at least one nucleotide; alternatively the overhang can comprise at least two nucleotides, at least three nucleotides, at least four nucleotides, at least five nucleotides, or more.
• a nucleotide overhang can comprise or consist of a nucleotide/nucleoside analog, including a deoxynucleotide/nucleoside.
• the overhang(s) can be on the sense strand, the antisense strand, or any combination thereof.
• the nucleotide(s) of an overhang can be present on the 5' end, 3' end, or both ends of either an antisense or sense strand of an siRNA.
• the antisense strand of an siRNA has a 1-10 nucleotide overhang at the 3' end and/or the 5' end. In some embodiments, the sense strand of an siRNA has a 1-10 nucleotide overhang at the 3' end and/or the 5' end. In some other embodiments, one or more of the nucleotides in the overhang is replaced with a nucleoside thiophosphate.
• siRNA or “blunt ended” as used herein in reference to an siRNA mean that there are no unpaired nucleotides or nucleotide analogs at a given terminal end of an siRNA, i.e., no nucleotide overhang.
• One or both ends of an siRNA can be blunt. Where both ends of an siRNA are blunt, the siRNA is said to be “blunt ended.”
• a “blunt ended” siRNA is an siRNA that is blunt at both ends, i.e., has no nucleotide overhang at either end of the molecule. Most often such a molecule will be double-stranded over its entire length.
• HBV gene expression in cell culture or expression of a cellular gene as a surrogate for HBV gene expression can be assayed by measuring HBV mRNA levels, such as by bDNA or TaqMan assay, or by measuring protein levels, such as by immunofluorescence analysis, using, for example, Western Blotting or flow cytometric techniques.
• An siRNA includes two RNA strands that are complementary and hybridize to form a duplex structure under conditions in which the siRNA will be used.
• One strand of an siRNA (the antisense strand) includes a region of complementarity that is substantially complementary, and generally fully complementary, to a target sequence.
• the target sequence can be derived from the sequence of an mRNA formed during the expression of an HBV gene.
• the other strand (the sense strand) includes a region that is complementary to the antisense strand, such that the two strands hybridize and form a duplex structure when combined under suitable conditions.
• the duplex structure is between 15 and 30 inclusive, more generally between 18 and 25 inclusive, yet more generally between 19 and 24 inclusive, and most generally between 19 and 21 base pairs in length, inclusive.
• a "part" of an mRNA target is a contiguous sequence of an mRNA target of sufficient length to be a substrate for RNAi-directed cleavage (i.e ., cleavage through a RISC pathway).
• siRNAs having duplexes as short as 9 base pairs can, under some circumstances, mediate RNAi-directed RNA cleavage.
• a target will be at least 15 nucleotides in length. In certain embodiments, the target is 15-30 nucleotides in length.
• the duplex region is a primary functional portion of an siRNA, e.g., a duplex region of 9 to 36, e.g., 15-30 base pairs.
• an RNA molecule or complex of RNA molecules having a duplex region greater than 30 base pairs is an siRNA.
• a miRNA is an siRNA.
• an siRNA is not a naturally occurring miRNA.
• an RNAi agent useful to target expression of an HBV gene is not generated in the target cell by cleavage of a larger double-stranded RNA.
• siRNA as described herein can be synthesized by standard methods known in the art, e.g., by use of an automated DNA synthesizer, such as are commercially available from, for example, Biosearch, Applied Biosystems, Inc.
• the RNAi agent comprises an siRNA that targets and inhibits expression of an HBV mRNA.
• the RNAi agent comprises an siRNA that targets and inhibits expression of an mRNA encoded by an HBV genome according to NCBI Reference Sequence NC_003977.2 (GenBank Accession No. GI:21326584) (SEQ ID NO:1). Transcription of the HBV genome results in polycistronic, overlapping RNAs, and therefore, in some embodiments, an siRNA of the combination therapy targeting a single HBV gene may result in significant inhibition of expression of most or all HBV transcripts.
• the siRNA targets and inhibits expression of an mRNA encoded by the X gene of HBV.
• the RNAi agent or siRNA targets an mRNA encoded by a portion of the HBV genome comprising the sequence GTGTGCACTTCGCTTCAC (SEQ ID NO:2), which corresponds to nucleotides 1579-1597 of NC_003977.2 (GenBank Accession No. GI:21326584) (SEQ ID NO:1).
• the inhibitor of HBV gene expression comprises an siRNA comprising a sense strand and an antisense strand, wherein the sense strand comprises SEQ ID NO:3, or a sequence that differs by not more than 4, not more than 3, not more than 2, or not more than 1 nucleotides from SEQ ID NO:3; and wherein the antisense strand comprises SEQ ID NO:4, or a sequence that differs by not more than 4, not more than 3, not more than 2, or not more than 1 nucleotides from SEQ ID NO:4,
• an siRNA will include at least two nucleotide sequences, a sense and an antisense sequence, whereby: the sense sequence comprises SEQ ID NO:3, and the corresponding antisense sequence comprises SEQ ID NO:4.
• one of the two sequences is complementary to the other of the two sequences, with one of the sequences being substantially complementary to a sequence of an mRNA generated in the expression of an HBV gene.
• an siRNA will include two oligonucleotides, where one oligonucleotide is described as the sense strand, and the second oligonucleotide is described as the corresponding antisense strand of the sense strand.
• the complementary sequences of an siRNA can also be contained as self-complementary regions of a single nucleic acid molecule, as opposed to being on separate oligonucleotides.
• the siRNA has a sense strand comprising 5'-GGUGGACUUCUCUCAAUUUUA -3' (SEQ ID NO:106) and an antisense strand comprising 5'- UAAAAUUGAGAGAAGUCCACCAC -3' (SEQ ID NO:107).
• the inhibitor of HBV gene expression comprises an siRNA comprising a sense strand and an antisense strand, wherein the sense strand comprises SEQ ID NO:106, or a sequence that differs by not more than 4, not more than 3, not more than 2, or not more than 1 nucleotides from SEQ ID NO:106; and wherein the antisense strand comprises SEQ ID NO: 107, or a sequence that differs by not more than 4, not more than 3, not more than 2, or not more than 1 nucleotides from SEQ ID NO: 107.
• an siRNA will include at least two nucleotide sequences, a sense and an antisense sequence, whereby: the sense sequence comprises SEQ ID NO:106, and the corresponding antisense sequence comprises SEQ ID NO: 107.
• one of the two sequences is complementary to the other of the two sequences, with one of the sequences being substantially complementary to a sequence of an mRNA generated in the expression of an HBV gene.
• an siRNA will include two oligonucleotides, where one oligonucleotide is described as the sense strand, and the second oligonucleotide is described as the corresponding antisense strand of the sense strand.
• the complementary sequences of an siRNA can also be contained as self-complementary regions of a single nucleic acid molecule, as opposed to being on separate oligonucleotides.
• siRNAs having a partial sequence of at least 15, 16, 17, 18, 19, 20, or more contiguous nucleotides from one or both of SEQ ID NO:106 and SEQ ID NO:107, and differing in their ability to inhibit the expression of an HBV gene by not more than 5, 10, 15, 20, 25, or 30 % inhibition from an siRNA comprising the full sequence, are contemplated according to the technology described herein.
• the RNAi agent includes at least 15 contiguous nucleotides from one or both of the sequences of SEQ ID NO: 106 and SEQ ID NO:107, coupled to additional nucleotide sequences taken from the region contiguous to the selected sequence in the HBV gene.
• target sequence is generally 15-30 nucleotides in length, there is wide variation in the suitability of particular sequences in this range for directing cleavage of any given target RNA.
• Various software packages and the guidelines set out herein provide guidance for the identification of optimal target sequences for any given gene target, but an empirical approach can also be taken in which a "window” or “mask” of a given size (as a non-limiting example, 21 nucleotides) is literally or figuratively (including, e.g., in silico ) placed on the target RNA sequence to identify sequences in the size range that can serve as target sequences.
• the next potential target sequence can be identified, until the complete set of possible sequences is identified for any given target size selected.
• This process coupled with systematic synthesis and testing of the identified sequences (using assays as described herein or as known in the art) to identify those sequences that perform optimally can identify those RNA sequences that, when targeted with an RNAi agent, mediate the best inhibition of target gene expression. It is contemplated that further optimization of inhibition efficiency can be achieved by progressively "walking the window" one nucleotide upstream or downstream of the given sequences to identify sequences with equal or better inhibition characteristics.
• any sequence identified e.g., SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO: 106, or SEQ ID NO: 107
• further optimization could be achieved by systematically either adding or removing nucleotides to generate longer or shorter sequences and testing those and sequences generated by walking a window of the longer or shorter size up or down the target RNA from that point.
• coupling this approach to generating new candidate targets with testing for effectiveness of RNAi agents based on those target sequences in an inhibition assay as known in the art or as described herein can lead to further improvements in the efficiency of inhibition.
• optimized sequences can be adjusted by, e.g., the introduction of modified nucleotides as described herein or as known in the art, addition or changes in overhang, or other modifications as known in the art and/or discussed herein to further optimize the molecule (e . g ., increasing serum stability or circulating half-life, increasing thermal stability, enhancing transmembrane delivery, targeting to a particular location or cell type, increasing interaction with silencing pathway enzymes, increasing release from endosomes, etc.) as an expression inhibitor.
• modified nucleotides as described herein or as known in the art, addition or changes in overhang, or other modifications as known in the art and/or discussed herein to further optimize the molecule (e . g ., increasing serum stability or circulating half-life, increasing thermal stability, enhancing transmembrane delivery, targeting to a particular location or cell type, increasing interaction with silencing pathway enzymes, increasing release from endosomes, etc.) as an expression inhibitor.
• RNAi agent as described herein can contain one or more mismatches to the target sequence. In some embodiments, an RNAi agent as described herein contains no more than 3 mismatches. In some embodiments, if the antisense strand of the RNAi agent contains mismatches to a target sequence, the area of mismatch is not located in the center of the region of complementarity. In particular embodiments, if the antisense strand of the RNAi agent contains mismatches to the target sequence, the mismatch is restricted to within the last 5 nucleotides from either the 5' or 3' end of the region of complementarity.
• RNAi agent RNA strand which is complementary to a region of an HBV gene
• the RNA strand may not contain any mismatch within the central 13 nucleotides.
• the methods described herein or methods known in the art can be used to determine whether an RNAi agent containing a mismatch to a target sequence is effective in inhibiting the expression of an HBV gene. Consideration of the efficacy of RNAi agents with mismatches in inhibiting expression of an HBV gene is important, especially if the particular region of complementarity in the HBV gene is known to have polymorphic sequence variation.
• the RNA of an RNAi agent e.g., an siRNA
• an RNAi agent e.g., an siRNA
• the nucleic acids featured in the technology described herein can be synthesized and/or modified by methods well established in the art, such as those described in " Current protocols in nucleic acid chemistry,” Beaucage, S.L., et al (Edrs), John Wiley & Sons, Inc., New York, NY, USA .
• Modifications include, for example, (a) end modifications, e . g ., 5' end modifications (phosphorylation, conjugation, inverted linkages, etc. ) , 3' end modifications (conjugation, DNA, nucleotides, inverted linkages, etc. ) , (b) base modifications, e . g ., replacement with stabilizing bases, destabilizing bases or bases that base pair with an expanded repertoire of partners, removal of bases (abasic nucleotides), or conjugated bases, (c) sugar modifications ( e . g ., at the 2' position or 4' position) or replacement of the sugar, as well as (d) backbone modifications, including modification or replacement of the phosphodiester linkages.
• end modifications e . g ., 5' end modifications (phosphorylation, conjugation, inverted linkages, etc. )
• 3' end modifications conjugation, DNA, nucleotides, inverted linkages, etc.
• base modifications e . g .
• RNA compounds useful in the embodiments described herein include, but are not limited to RNAs containing modified backbones or no natural internucleoside linkages.
• RNAs having modified backbones include, among others, those that do not have a phosphorus atom in the backbone.
• modified RNAs that do not have a phosphorus atom in their internucleoside backbone can also be considered to be oligonucleosides.
• the modified RNA will have a phosphorus atom in its internucleoside backbone.
• RNAi agent compounds that are chimeric compounds.
• "Chimeric" RNAi agent compounds or “chimeras,” in the context of this disclosure, are RNAi agent compounds, such as siRNAs, which contain two or more chemically distinct regions, each made up of at least one monomer unit, i.e., a nucleotide in the case of an siRNA compound.
• RNAi agents typically contain at least one region wherein the RNA is modified so as to confer upon the RNAi agent increased resistance to nuclease degradation, increased cellular uptake, and/or increased binding affinity for the target nucleic acid.
• An additional region of the RNAi agent can serve as a substrate for enzymes capable of cleaving RNA:DNA or RNA:RNA hybrids.
• RNase H is a cellular endonuclease which cleaves the RNA strand of an RNA:DNA duplex. Activation of RNase H, therefore, results in cleavage of the RNA target, thereby greatly enhancing the efficiency of RNAi agent inhibition of gene expression.
• RNAi agents when chimeric siRNAs are used, compared to phosphorothioate deoxy siRNAs hybridizing to the same target region. Cleavage of the RNA target can be routinely detected by gel electrophoresis and, if necessary, associated nucleic acid hybridization techniques known in the art.
• Modified RNA backbones include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl phosphonates including 3'-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3'-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates having normal 3'-5' linkages, 2'-5' linked analogs of these, and those) having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3'-5' to 5'-3' or 2'-5' to 5'-2'.
• Various salts, mixed salts, and free acid forms are also included.
• Modified RNA backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatoms and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages.
• morpholino linkages formed in part from the sugar portion of a nucleoside
• siloxane backbones sulfide, sulfoxide and sulfone backbones
• formacetyl and thioformacetyl backbones methylene formacetyl and thioformacetyl backbones
• alkene containing backbones sulfamate backbones
• sulfonate and sulfonamide backbones amide backbones; and others having mixed N, O, S, and CH2 component parts.
• U.S. patents that teach the preparation of the above oligonucleosides include, but are not limited to, U.S. Patent Nos. 5,034,506 ; 5,166,315 ; 5,185,444 ; 5,214,134 ; 5,216,141 ; 5,235,033 ; 5,64,562 ; 5,264,564 ; 5,405,938 ; 5,434,257 ; 5,466,677 ; 5,470,967 ; 5,489,677 ; 5,541,307 ; 5,561,225 ; 5,596,086 ; 5,602,240, 5,608,046 ; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437 ; and 5,677,439 .
• RNA mimetics suitable are contemplated for use in RNAi agents, in which both the sugar and the internucleoside linkage, i.e., the backbone, of the nucleotide units are replaced with novel groups,
• the base units are maintained for hybridization with an appropriate nucleic acid target compound.
• a peptide nucleic acid PNA
• PNA peptide nucleic acid
• the sugar backbone of an RNA is replaced with an amide containing backbone, in particular an aminoethyglycine backbone.
• the nucleobases are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone.
• TNAs with phosphorothioate backbones and oligonucleosides with heteroatom backbones and in particular -CH 2 -NH-CH 2- , -CH 2 -N(CH 3 )-O-CH 2 -[known as a methylene (methylamino) or MMI backbone], -CH 2 -O-N(CH 3 )-CH 2 -, -CH 2 -N(CH 3 )-N(CH 3 )-CH 2 -, and -N(CH 3 )-CH 2 -CH 2 - [wherein the native phosphodiester backbone is represented as - O-P-O-CH 2- ] of U.S. Pat.
• RNAs featured herein have morpholino backbone structures of U.S. Pat. No. 5,034,506 .
• RNAs can also contain one or more substituted sugar moieties.
• the RNAi agents e.g., siRNAs, featured herein can include one of the following at the 2' position: OH; F;O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or O-alkyl-O-alkyl; wherein the alkyl alkenyl, and alkynyl can be substituted or Unsubstituted C 1 to C 10 alkyl or C 2 to C 10 alkenyl and alkynyl.
• Exemplary suitable modifications include O[(CH 2 ) n O] m CH 3 , O(CH 2 ).
• siRNAs include one of the following at the 2' position: C 1 to C 10 lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH 3 , OCN, CI, Br, CN, CF 3 , OCF 3 , SOCH 3 , SO 2 CH 3 , ONO 2 , NO 2 , N 3 , NH 2 , heterocycloalkyl, heterocycloalkaryl, aminoalkulamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an RNAi agent, or a group for improving the pharmacodynamic properties of an RNAi agent, and other substitutes having similar properties.
• the modification includes a 2'-methoxyethoxy (2'-O-CH 2 CH 2 OCH 3 , also known as 2'-O-(2-methoxyethyl) or 2'-MOE) ( Martin, et al., Helv. Chim. Acta 78:486-504 (1995 )), i.e., an alkoxy-alkoxy group.
• 2'-methoxyethoxy 2'-O-CH 2 CH 2 OCH 3
• 2'-MOE 2'-methoxyethoxy
• Another exemplary modification is 2'- dimethylaminooxyethoxy, i.e., a O(CH 2 ) 2 ON(CH 3 ) 2 group, also known as 2'-DMAOE, and 2'-dimethylaminoethoxyethoxy (also known in the art as 2*-O-dimethylaminoethoxyethyl or 2*-DMAEOE), i.e., 2*-O-CH 2 -O-CH 2 -N(CH 2 ) 2 .
• 2'- dimethylaminooxyethoxy i.e., a O(CH 2 ) 2 ON(CH 3 ) 2 group, also known as 2'-DMAOE
• 2'-dimethylaminoethoxyethoxy also known in the art as 2*-O-dimethylaminoethoxyethyl or 2*-DMAEOE
• RNAi agents can also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar.
• RNAi agent can also include nucleobase (often referred to in the art simply as “base”) modifications or substitutions.
• nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C), and uracil (U).
• Modified nucleobases include other synthetic and natural nucleobases such as 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytisone, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5 -uracil (pseudouracil), 4-thiouracil, 8-halo, ,8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo, particularly 5-bromo, 5-trifluoromethyl
• nucleobases are particularly useful for increasing the binding affinity of the oligomeric compounds featured in the technology described herein.
• These include 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6, and O-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. 5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2°C ( Sanghvi, Y.S., Crooke, S. T.
• U.S. Patents that teach the preparation of locked nucleic acid nucleotides include, but are not limited to, the following: U.S. Pat. Nos. 6,268,490 ; 6,670,461 ; 6,794,499 ; 6,998,484 ; 7,053,207 ; 7,084,125 ; and 7,399,845 .
• the combination therapy includes an siRNA that is modified to include one or more adenosine-glycol nucleic acid (“GNA").
• GAA adenosine-glycol nucleic acid
• the inhibitor of HBV gene expression comprises an siRNA, wherein the siRNA has a sense strand comprising 5'-gsusguGfcAfCfUfucgcuucacaL96 -3' (SEQ ID NO:5) and an antisense strand comprising 5'- usGfsugaAfgCfGfaaguGfcAfcacsusu -3' (SEQ ID NO:6).
• the siRNA has a sense strand comprising 5'-gsusguGfcAfCfUfucgcuucacaL96-3' (SEQ ID NO:7) and an antisense strand comprising 5'-usGfsuga(Agn)-CfGfaaguGfcAfcacsusu-3' (SEQ ID NO:8).
• the inhibitor of HBV gene expression comprises an siRNA comprising a sense strand and an antisense strand, wherein the sense strand comprises SEQ ID NO:5 or SEQ ID NO:7, or a sequence that differs by not more than 4, not more than 3, not more than 2, or not more than 1 nucleotide from SEQ ID NO: 5 or SEQ ID NO:7, respectively.
• the inhibitor of HBV gene expression comprises an siRNA, wherein the siRNA has a sense strand comprising 5'-gsgsuggaCfuUfCfUfcucaAfUfuuuaL96-3' (SEQ ID NO:108) and an antisense strand comprising 5'-usAfsaaaUfuGfAfgagaAfgUfccaccsasc-3' (SEQ ID NO:109).
• Ligands can include a naturally occurring substance, such as a protein (e.g., human serum albumin (HSA), low-density lipoprotein (LDL), or globulin); carbohydrate ( e.g ., a dextran, pullulan, chitin, chitosan, inulin, cyclodextrin, or hyaluronic acid); or a lipid.
• HSA human serum albumin
• LDL low-density lipoprotein
• globulin carbohydrate
• carbohydrate e.g ., a dextran, pullulan, chitin, chitosan, inulin, cyclodextrin, or hyaluronic acid
• the ligand can also be a recombinant or synthetic molecule, such as a synthetic polymer, e.g ., a synthetic polyamino acid.
• polyamino acids examples include polyamino acid is a polylysine (PLL), poly L-aspartic acid, poly L-glutamic acid, styrene-maleic acid anhydride copolymer, poly(L-lactide-co-glycolied) copolymer, divinyl ether-maleic anhydride copolymer, N-(2-hydroxypropyl)methacrylamide copolymer (MIPA), polyethylene glycol (PEG), polyvinyl alcohol (PVA), polyurethane, poly(2-ethylacryllic acid), N-isopropylacrylamide polymers, or polyphosphazine.
• PLL polylysine
• poly L-aspartic acid poly L-glutamic acid
• styrene-maleic acid anhydride copolymer poly(L-lactide-co-glycolied) copolymer
• divinyl ether-maleic anhydride copolymer divinyl ether-
• polyamines include: polyethylenimine, polylysine (PLL), spermine, spermidine, polyamine, pseudopeptide-polyamine, peptidomimetic polyamine, dendrimer polyamine, arginine, amidine, protamine, cationic lipid, cationic porphyrin, quaternary salt of a polyamine, or an alpha helical peptide.
• Ligands can also include targeting groups, e.g ., a cell or tissue targeting agent, e.g., a lectin, glycoprotein, lipid or protein, e.g ., an antibody, that binds to a specified cell type such as a liver cell.
• a cell or tissue targeting agent e.g., a lectin, glycoprotein, lipid or protein, e.g ., an antibody, that binds to a specified cell type such as a liver cell.
• a targeting group can be a thyrotropin, melanotropin, lectin, glycoprotein, surfactant protein A, Mucin carbohydrate, multivalent lactose, multivalent galactose, N-acetyl-galactosamine, N-acetyl-gulucosamine multivalent mannose, multivalent fucose, glycosylated polyaminoacids, multivalent galactose, transferrin, bisphosphonate, polyglutamate, polyaspartate, a lipid, cholesterol, a steroid, bile acid, folate, vitamin B12, vitamin A, biotin, or an RGD peptide or RGD peptide mimetic.
• imidazole bisimidazole, histamine, imidazole clusters, acridine-imidazole conjugates, Eu3+ complexes of tetraazamacrocycles), dinitrophenyl, HRP, and AP.
• Ligands can be proteins, e.g. , glycoproteins, or peptides, e.g ., molecules having a specific affinity for a co-ligand, or antibodies e.g ., an antibody, that binds to a specified cell type such as a hepatic cell.
• Ligands can also include hormones and hormone receptors. They can also include non-peptidic species, such as lipids, lectins, carbohydrates, vitamins, cofactors, multivalent lactose, multivalent galactose, N-acetyl-galactosamine, N-acetyl- gulucosamine multivalent mannose, and multivalent fucose.
• the ligand can be, for example, a lipopolysaccharide, an activator of p38 MAP kinase, or an activator of NF-KB.
• the ligand can be a substance, e.g., a drug, which can increase the uptake of the RNAi agent into the cell, for example, by disrupting the cell's cytoskeleton, e . g ., by disrupting the cell's microtubules, microfilaments, and/or intermediate filaments.
• the drug can be, for example, taxon, vincristine, vinblastine, cytochalasin, nocodazole, japlakinolide, latrunculin A, phalloidin, swinholide A, indanocine, or myoservin.
• the ligand is a moiety, e . g ., a vitamin, which is taken up by a target cell, e.g., a liver cell.
• a target cell e.g., a liver cell.
• exemplary vitamins include vitamin A, E, and K.
• Other exemplary vitamins include are B vitamin, e . g ., folic acid, B12, riboflavin, biotin, pyridoxal, or other vitamins or nutrients taken up by target cells such as liver cells.
• Oligonucleotides that comprise a number of phosphorothioate linkages are also known to bind to serum protein, thus short oligonucleotides, e . g ., oligonucleotides of about 5 bases, 10 bases, 15 bases, or 20 bases, comprising multiple of phosphorothioate linkages in the backbone are also amenable to the technology described herein as ligands (e.g., as PK modulating ligands).
• ligands e.g., as PK modulating ligands
• aptamers that bind serum components e. g ., serum proteins
• PK modulating ligands are also suitable for use as PK modulating ligands in the embodiments described herein.
• the lipid based ligand binds HSA.
• the lipid based ligand may bind to HSA with a sufficient affinity such that the conjugate will be distributed to a non-kidney tissue.
• the HSA-ligand binding is reversible.
• the ligand is a cell-permeation agent, such as a helical cell-permeation agent.
• the agent is amphipathic.
• An exemplary agent is a peptide such as tat or antennopedia. If the agent is a peptide, it can be modified, including a peptidylmimetic, invertomers, non-peptide or pseudo-peptide linkages, and use of D-amino acids.
• the helical agent is an alpha-helical agent. In certain particular embodiments, the helical agent has a lipophilic and a lipophobic phase.
• a "cell permeation peptide” is capable of permeating a cell, e.g., a microbial cell, such as a bacterial or fungal cell, or a mammalian cell, such as a human cell.
• a microbial cell-permeating peptide can be, for example, an alpha-helical linear peptide (e.g., LL-37 or Ceropin PI), a disulfide bond-containing peptide (e.g., a-defensin, ⁇ -defensin, or bactenecin), or a peptide containing only one or two dominating amino acids ( e . g ., PR-39 or indolicidin).
• an alpha-helical linear peptide e.g., LL-37 or Ceropin PI
• a disulfide bond-containing peptide e.g., a-defensin, ⁇ -defensin, or
• the ligand can be a peptide or peptidomimetic.
• a peptidomimetic also referred to herein as an oligopeptidomimetic is a molecule capable of folding into a defined three-dimensional structure similar to a natural peptide.
• the attachment of peptide and peptidomimetics to RNAi agents can affect pharmacokinetic distribution of the RNAi, such as by enhancing cellular recognition and absorption.
• the peptide or peptidomimetic moiety can be about 5-50 amino acids long, e.g., about 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids long.
• a peptide or peptidomimetic can be, for example, a cell permeation peptide, cationic peptide, amphipathic peptide, or hydrophobic peptide (e.g., consisting primarily of Tyr, Trp or Phe).
• the peptide moiety can be a dendrimer peptide, constrained peptide or crosslinked peptide.
• the peptide moiety can include a hydrophobic membrane translocation sequence (MTS).
• An exemplary hydrophobic MTS-containing peptide is RFGF having the amino acid sequence AAVALLPAVLLALLAP (SEQ ID NO:9).
• An RFGF analogue e.g., amino acid sequence AALLPVLLAAP (SEQ ID NO: 10) containing a hydrophobic MTS can also be a targeting moiety.
• the peptide moiety can be a "delivery" peptide, which can carry large polar molecules including peptides, oligonucleotides, and proteins across cell membranes.
• sequences from the HIV Tat protein GRKKRRQRRRPPQ (SEQ ID NO:11) and the Drosophila Antennapedia protein (RQIKIWFQNRRMKWK (SEQ ID NO:12) have been found to be capable of functioning as delivery peptides.
• a peptide or peptidomimetic can be encoded by a random sequence of DNA, such as a peptide identified from a phage-display library, or one-bead-one- compound (OBOC) combinatorial library ( Lam, et al., Nature 354:82-84 (1991 )).
• OBOC one-bead-one- compound
• a cell permeation peptide can also include a nuclear localization signal (NLS).
• NLS nuclear localization signal
• a cell permeation peptide can be a bipartite amphipathic peptide, such as MPG, which is derived from the fusion peptide domain of HIV- 1 gp41 and the NLS of SV40 large T antigen ( Simeoni, et al., Nucl. Acids Res. 31:2717-24 (2003 )).
• RNAi agent oligonucleotides described herein further comprise carbohydrate conjugates.
• the carbohydrate conjugates may be advantageous for the in vivo delivery of nucleic acids, as well as compositions suitable for in vivo therapeutic use.
• carbohydrate refers to a compound which is either a carbohydrate per se made up of one or more monosaccharide units having at least 6 carbon atoms (which can be linear, branched, or cyclic) with an oxygen, nitrogen, or sulfur atom bonded to each carbon atom; or a compound having as a part thereof a carbohydrate moiety made up of one or more monosaccharide units each having at least six carbon atoms (which can be linear, branched, or cyclic), with an oxygen, nitrogen, or sulfur atom bonded to each carbon atom.
• Representative carbohydrates include the sugars (mono-, di-, tri-, and oligosaccharides containing from about 4-9 monosaccharide units), and polysaccharides such as starches, glycogen, cellulose, and polysaccharide gums.
• Specific monosaccharides include C5 and above (in some embodiments, C5-C8) sugars; and di- and trisaccharides include sugars having two or three monosaccharide units (in some embodiments, C5-C8).
• the carbohydrate conjugate is selected from the group consisting of:
• the carbohydrate conjugate further comprises another ligand such as, but not limited to, a PK modulator, an endosomolytic ligand, or a cell permeation peptide.
• another ligand such as, but not limited to, a PK modulator, an endosomolytic ligand, or a cell permeation peptide.
• the conjugates described herein can be attached to the RNAi agent oligonucleotide with various linkers that can be cleavable or non-cleavable.
• linker or “linking group” means an organic moiety that connects two parts of a compound.
• Linkers typically comprise a direct bond or an atom such as oxygen or sulfur, a unit such as NR8, C(O), C(O)NH, SO, SO2, SO2NH, or a chain of atoms, such as, but not limited to, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, arylalkyl, arylalkenyl, arylalkynyl, heteroarylalkyl, heteroarylalkenyl, heteroarylalkynyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, aryl, heteroaryl, heterocyclyl, cycloalkyl, cycloalkenyl, alkylarylalkyl, alkylarylalkenyl, alkylarylalken
• degradative agents include: redox agents which are selected for particular substrates or which have no substrate specificity, including, e.g ., oxidative or reductive enzymes or reductive agents such as mercaptans, present in cells, that can degrade a redox cleavable linking group by reduction; esterases; endosomes or agents that can create an acidic environment, e.g ., those that result in a pH of five or lower; enzymes that can hydrolyze or degrade an acid cleavable linking group by acting as a general acid, peptidases (which can be substrate specific), and phosphatases.
• a cleavable linkage group, such as a disulfide bond can be susceptible to pH.
• the pH of human serum is 7.4, while the average intracellular pH is slightly lower, ranging from about 7.1-7.3. Endosomes have a more acidic pH, in the range of 5.5-6.0, and lysosomes have an even more acidic pH at around 5.0. Some linkers will have a cleavable linking group that is cleaved at a particular pH, thereby releasing the cationic lipid from the ligand inside the cell, or into the desired compartment of the cell.
• useful candidate compounds are cleaved at least 2, at least 4, at least 10 or at least 100 times faster in the cell (or under in vitro conditions selected to mimic intracellular conditions) as compared to blood or serum (or under in vitro conditions selected to mimic extracellular conditions).
• cleavable linking groups are redox cleavable linking groups that are cleaved upon reduction or oxidation.
• An example of reductively cleavable linking group is a disulphide linking group (-S-S-).
• a candidate cleavable linking group is a suitable "reductively cleavable linking group," or for example is suitable for use with a particular RNAi moiety and particular targeting agent one can look to methods described herein.
• Phosphate-based cleavable linking groups are cleaved by agents that degrade or hydrolyze the phosphate group.
• An example of an agent that cleaves phosphate groups in cells are enzymes such as phosphatases in cells.
• phosphate-based linking groups are -O-P(O)(ORk)-O-, -O-P(S)(ORk)-O-, -O-P(S)(SRk)-O-, -S-P(O)(ORk)-O-, -O- P(O)(ORk)-S-, -S-P(O)(ORk)-S-, -O-P(S)(ORk)-S-, -O-P(S)(ORk)-S-, -S-P(S)(ORk)-O-, -O-P(O)(Rk)-O-, -O- P(S)(Rk)-O-, -S-
• the phosphate-based linking groups are selected from: -O-P(O)(OH)-O-, -O-P(S)(OH)-O-, -O-P(S)(SH)-O-, -S-P(O)(OH)-O-, - O- P(0)(OH)-S-, -S-P(O)(OH)-S-, -O-P(S)(OH)-S-, -S-P(S)(OH)-O-, -O-P(S)(OH)-O-, -O-P(O)(H)-O-, - O- P(S)(H)-O-, -S-P(O)(H)-O-, -S-P(S)(H)-O-, -S-P(O)(H)-S-, and -O-P(S)(H)-S-.
• the phosphate-linking group is -O-P(O
• Acid cleavable linking groups are linking groups that are cleaved under acidic conditions.
• acid cleavable linking groups are cleaved in an acidic environment with a pH of about 6.5 or lower ( e.g., about 6.0, 5.5, 5.0, or lower), or by agents such as enzymes that can act as a general acid.
• specific low pH organelles such as endosomes and lysosomes, can provide a cleaving environment for acid cleavable linking groups.
• acid cleavable linking groups include but are not limited to hydrazones, esters, and esters of amino acids.
• the carbon attached to the oxygen of the ester is an aryl group, substituted alkyl group, or tertiary alkyl group such as dimethyl pentyl or t-butyl.
• Ester-based cleavable linking groups are cleaved by enzymes such as esterases and amidases in cells.
• Examples of ester-based cleavable linking groups include but are not limited to esters of alkylene, alkenylene, and alkynylene groups.
• Ester cleavable linking groups have the general formula -C(O)O-, or -OC(O)-. These candidates can be evaluated using methods analogous to those described above.
• Peptide-based cleavable linking groups are cleaved by enzymes such as peptidases and proteases in cells.
• Peptide-based cleavable linking groups are peptide bonds formed between amino acids to yield oligopeptides ( e.g., dipeptides, tripeptides, etc .) and polypeptides.
• Peptide-based cleavable groups do not include the amide group (-C(O)NH-).
• the amide group can be formed between any alkylene, alkenylene, or alkynelene.
• a peptide bond is a special type of amide bond formed between amino acids to yield peptides and proteins.
• the peptide based cleavage group is generally limited to the peptide bond (i.e., the amide bond) formed between amino acids yielding peptides and proteins and does not include the entire amide functional group.
• Peptide-based cleavable linking groups have the general formula - NHCHRAC(O)NHCHRBC(O)-, where RA and RB are the R groups of the two adjacent amino acids. These candidates can be evaluated using methods analogous to those described above.
• Representative carbohydrate conjugates with linkers include, but are not limited to, and wherein when one of X or Y is an oligonucleotide, the other is a hydrogen.
• the combination therapy includes an siRNA that is conjugated to a bivalent or trivalent branched linker selected from the group of structures shown in any of formula (XXXI) - (XXXIV): wherein:
• Suitable bivalent and trivalent branched linker groups conjugating GalNAc derivatives include, but are not limited to, the structures recited above as formulas I, VI, X, IX, and XII.
• a thioether e.g. , hexyl-S-tritylthiol ( Manoharan, et al., Ann. N.Y. Acad. Sci. 660:306 (1992 ); Manoharan, et al., Bioorg. Med. Chem. Let. 3:2765 (1993 )), a thiocholesterol ( Oberhauser, et al., Nucl. Acids Res. 20:533 (1992 )), an aliphatic chain, e.g ., dodecandiol or undecyl residues ( Jerusalem-Behmoaras, et al., EMBO J.
• Typical conjugation protocols involve the synthesis of an RNAs bearing in aminolinker at one of more positions of the sequence. The amino group is then reacted with the molecule being conjugated using appropriate coupling or activating reagents.
• the conjugation reaction can be performed either with the RNA still bound to the solid ;support or following cleavage of the RNA, in solution phase. Purification of the RNA conjugate by HPLC typically affords the pure conjugate.
• RNAi agent means facilitating or effecting uptake or absorption into the cell, as is understood by those skilled in the art.
• RNAi agent to a subject in need thereof can be achieved in a number of different ways. In vivo delivery can be performed directly by administering a composition comprising an RNAi agent, e.g.., an siRNA, to a subject. Alternatively, delivery can be performed indirectly by administering one or more vectors that encode and direct the expression of the RNAi agent. These alternatives are discussed further below.
• RNAi agent Several studies have shown successful knockdown of gene products when an RNAi agent is administered locally. For example, intraocular delivery of a VEGF siRNA by intravitreal injection in cynomolgus monkeys ( Tolentino, M.J., et al., Retina 24:132-38 (2004 )) and subretinal injections in mice ( Reich, S.J., et al., Mol. Vis.
• RNAi agent for administering an RNAi agent systemically for the treatment of a disease, the RNA can be modified or alternatively delivered using a drug delivery system; both methods act to prevent the rapid degradation of the siRNA by endo- and exo-nucleases in vivo.
• RNAi agents can be modified by chemical conjugation to lipophilic groups such as cholesterol to enhance cellular uptake and prevent degradation.
• lipophilic groups such as cholesterol to enhance cellular uptake and prevent degradation.
• an RNAi agent directed against ApoB conjugated to a lipophilic cholesterol moiety was injected systemically into mice and resulted in knockdown of apoB mRNA in both the liver and jejunum ( Soutschek, J., et al., Nature 4432:173-78 (2004 )).
• the RNAi agent can be delivered using drug delivery systems such as a nanoparticle, a dendrimer, a polymer, liposomes, or a cationic delivery system.
• Positively charged cationic delivery systems typically facilitate binding of an RNAi agent (negatively charged) and enhance interactions at the negatively charged cell membrane to permit efficient uptake of an RNAi agent by the cell.
• Cationic lipids, dendrimers, or polymers can either be bound to an RNAi, or induced to form a vesicle or micelle ( see, e.g., Kim, S,H., et al., Journal of Controlled Release 129(2):107-16 (2008 )) that encases an RNAi agent.
• vesicles or micelles further prevents degradation of the RNAi agent when administered systemically.
• Methods for making and administering cationic-RNAi agent complexes are well within the abilities of one skilled in the art (see, e.g., Sorensen, D.R., et al., J. Mol. Biol. 327:761-66 (2003 ): Verma, U.N., et al., Clin. Cancer Res. 9:1291-1300 (2003 ): Arnold, A.S. et al., J. Hypertens. 25:197-205 (2007 ).
• RNAi agents include DOTAP (Sorensen, D.R., et al. (2003), supra; Verma, U.N., et al., (2003), supra ), Oligofectamine, "solid nucleic acid lipid particles" ( Zimmermann, T.S., et al., Nature 441:111-14 (2006 )), cardiolipin ( Chien, P.Y, et al., Cancer Gene Ther. 12:3211-28 (2005 ); Pal. A., et al., Int J. Oncol. 26: 1087-91 (2005 )), polyethylenimine ( Bonnet, M.E., et al., Pharm.
• SNALP refers to a stable nucleic acid-lipid particle.
• a SNALP represents a vesicle of lipids coating a reduced aqueous interior comprising a nucleic acid such as an RNAi agent or a plasmid from which an RNAi agent is transcribed.
• SNALPs are described, e.g. in U.S. Patent Application Publication Nos. US2006/0240093 and US2007/0135372 , and in International Application Publication No. WO 2009/082817 .
• an RNAi forms a complex with cyclodextrin for systemic administration.
• Methods for administration and pharmaceutical compositions of RNAis and cyclodextrins can be found in U.S. Pat. No. 7, 427, 605 .
• a gene encoding an RNAi is encoded and expressed from an expression vector. Examples of vectors and their use in deliverying RNAis are described in U.S. Patent Application No. US2017/0349900A1 .
• Typical pharmaceutically acceptable carriers or excipients include, but are not limited to, binding agents (e.g., pregelatinized maize starch, polyvinylpyrrolidone, hydroxypropyl methylcellulose); fillers ( e.g., lactose and other sugars, microcrystalline cellulose, pectin, gelatin, calcium sulfate, ethyl cellulose, polyacrylates, calcium hydrogen phosphate); lubricants (e.g., magnesium stearate, talc, silica, colloidal silicon dioxide, stearic acid, metallic stearates, hydrogenated vegetable oils, corn starch, polyethylene glycols, sodium benzoate, sodium acetate); disintegrants ( e.g., starch, sodium starch glycolate); and wetting agents (e.g., sodium lauryl sulphate).
• binding agents e.g., pregelatinized maize starch, polyvinylpyrrolidone, hydroxypropyl methylcellulose
• Suitable pharmaceutically acceptable excipients include, but are not limited to, water, salt solutions, alcohol, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose, polyvinylpyrrolidone, and the like.
• the pharmaceutical composition can be administered once daily, or the RNAi agent can be administered as two, three, or more sub-doses at appropriate intervals throughout the day or even using continuous infusion or delivery through a controlled release formulation. In that case, the RNAi agent contained in each sub-dose must be correspondingly smaller in order to achieve the total daily dosage.
• the dosage unit can also be compounded for delivery over several days, e.g., using a conventional sustained release formulation which provides sustained release of the RNAi over a several day period. Sustained release formulations are well known in the art and are particularly useful for delivery of agents at a particular site, such as could be used with the agents of the technology described herein. In this embodiment, the dosage unit contains a corresponding multiple of the daily dose.
• RNAi agents can influence the dosage and timing required to effectively treat a subject, including but not limited to the severity of the disease or disorder, previous treatments, the general health and/or age of the subject, and other diseases present.
• treatment of a subject with a therapeutically effective amount of a composition can include a single treatment or a series of treatments.
• Estimates of effective dosages and in vivo half-lives for the individual RNAi agents encompassed by the technology described herein can be made using conventional methodologies or on the basis of in vivo testing using an appropriate animal model, as described elsewhere herein.
• Mouse models are available for the study of HBV infection, and such models can be used for in vivo testing of RNAi, as well as for determining a dose that is effective at reducing HBV gene expression.
• an RNAi agent used in a combination therapy for treating HBV as disclosed herein is delivered subcutaneously.
• Suitable lipids and liposomes include neutral (e.g., dioleoylphosphatidyl DOPE ethanolamine, dimyristoylphosphatidyl choline DMPC, distearolyphosphatidyl choline), negative (e.g., dimyristoylphosphatidyl glycerol DMPG), and cationic (e.g., dioleoyltetramethylaminopropyl DOTAP and dioleoylphosphatidyl ethanolamine DOTMA).
• RNAi agents can be encapsulated within liposomes or can form complexes thereto, in particular to cationic liposomes.
• Vesicles such as liposomes, may be used in formulations for delivering RNAi agents disclosed herein.; such formulation may have desirable properties such as specificity and the duration of action.
• liposome means a vesicle composed of amphiphilic lipids arranged in a spherical bilayer or bilayers.
• Liposomes fall into two broad classes. Cationic liposomes are positively charged liposomes which interact with the negatively charged nucleic acid molecules to form a stable complex. The positively charged DNA/liposome complex binds to the negatively charged cell surface and is internalized in an endosome. Due to the acidic pH within the endosome, the liposomes are ruptured, releasing their contents into the cell cytoplasm ( Wang, et al., Biochem. Biophys. Res. Commun. 147, 980-985 (1987 )).
• liposomal drug formulations are delivered topically to the skin.
• SNALPs and SPLPs typically contain a cationic lipid, a non-cationic lipid, and a lipid that prevents aggregation of the particle (e.g., a PEG-lipid conjugate).
• SNALPs and SPLPs may be used for systemic applications, as they exhibit extended circulation lifetimes following intravenous (i.v.) injection and accumulate at distal sites (e.g., sites physically separated from the administration site).
• SPLPs include "pSPLP," which include an encapsulated condensing agent-nucleic acid complex as set forth in International Application Publication No. WO 00/03683 .
• S-HBsAg, M-HBsAg, and L- HBsAg share the same C-terminal extremity (also referred to as "S domain", 226 amino acids), which corresponds to the S protein (S-HBsAg) and which is involved in virus assembly and infectivity.
• S-HBsAg, M-HBsAg, and L-HBsAg are synthesized in the endoplasmic reticulum (ER), assembled, and secreted as particles through the Golgi apparatus.
• the S domain comprises four predicted transmembrane (TM) domains, whereby both the N-terminus and the C-terminus of the S domain are exposed to the lumen.
• corresponding sequence fragments refers to fragments that are located in equal positions of sequences when the sequences are subjected to optimized alignment, namely, the sequences are aligned to obtain a highest percentage of identity.
• the M protein corresponds to the S protein extended by an N-terminal domain of 55 amino acids called "pre-S2".
• the L protein (L-HBsAg) corresponds to the M protein extended by an N-terminal domain of 108 amino acids called "pre-S1" (genotype D).
• the pre-S1 and pre-S2 domains of the L protein can be present either at the inner face of viral particles (on the cytoplasmic side of the ER), playing a crucial role in virus assembly, or on the outer face (on the luminal side of the ER), available for the interaction with target cells and necessary for viral infectivity.
• HBV surface proteins HBsAgs
• SVPs empty "subviral particles”
• all three HBV envelope proteins S-HBsAg, M-HBsAg, and L-HBsAg comprise the S domain
• all three HBV envelope proteins S-HBsAg, M-HBsAg, and L-HBsAg also comprise the "antigenic loop region". Accordingly, an antibody or an antigen binding fragment thereof that binds to the antigenic loop region of HBsAg binds to all three HBV envelope proteins: S-HBsAg, M-HBsAg, and L-HBsAg.
• an antibody according to the present disclosure, or an antigen binding fragment thereof promotes clearance of HBsAg and HBV.
• an antibody according to the present disclosure, or an antigen binding fragment thereof may promote clearance of both HBV and subviral particles of hepatitis B virus (SVPs).
• Clearance of HBsAg or of subviral particles may be assessed by measuring the level of HBsAg for example in a blood sample, e.g., from a hepatitis B patient.
• clearance of HBV may be assessed by measuring the level of HBV for example in a blood sample, e.g ., from a hepatitis B patient.
• an excess of subviral particles can serve as a decoy by absorbing neutralizing antibodies and therefore delay the clearance of infection.
• achievement of hepatitis B surface antigen (HBsAg) loss is thus considered to be an ideal endpoint of treatment and the closest outcome to cure chronic hepatitis B (CHB).
• an antibody according to the present disclosure, or an antigen binding fragment thereof, which promotes clearance of HBsAg, and in particular, clearance of subviral particles of hepatitis B virus and HBV enables improved treatment of hepatitis B, in particular in the context of chronic hepatitis B.
• an antibody according to the present disclosure, or an antigen binding fragment thereof binds to at least 6, to at least 8, or to all 10 of the HBsAg genotypes A, B, C, D, E, F, G, H, I, and J. In certain embodiments, an antibody according to the present disclosure, or an antigen binding fragment thereof, binds to 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 of the HBsAg genotypes A, B, C, D, E, F, G, H, I, and J.
• Examples for the different genotypes of HBsAg include the following: GenBank accession number J02203 (HBV-D, ayw3), GenBank accession number FJ899792.1 (HBV-D, adw2), GenBank accession number AM282986 (HBV-A), GenBank accession number D23678 (HBV-B1 Japan), GenBank accession number AB1 1 7758 (FMV-C1 Cambodia), GenBank accession number AB205192 (HBV-E Ghana), GenBank accession number X69798 (HBV-F4 Brazil), GenBank accession number AF160501 (HBV-G USA), GenBank accession number AY090454 (HBV-H Portugal), GenBank accession number AF241409 (HBV-I Vietnam), and GenBank accession number AB486012 (HBV-J Borneo).
• an antibody according to the present disclosure binds to 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17 or 18 of the HBsAg mutants having mutations in the antigenic loop region: HBsAg Y100C/PI20T, HBsAg P120T, HBsAg P120T/S143L, HBsAg C121 S, HBsAg R122D, HBsAg R122I, HBsAg T123N, HBsAg Q129H, HBsAg Q129L, HBsAg M133H, HBsAg M133L, HBsAg M133T, HBsAg K141 E, HBsAg P142S, HBsAg S143K, HBsAg D144A, HBsAg G145R, and HBsAg N146A.
• mutants are naturally occurring mutants based on the S domain of HBsAg Genotype D (SEQ ID NO:43), Genbank accession no. FJ899792 (whereby the mutated amino acid residue(s) are indicated in the name).
• MENVTSGFLGPLLVLQAGFFLLTRILTIPQSLDSWWTSLNFLGGT TVCLGQNSQSPTSNHSPTS CPPTCPGYRWNICLRRFIIFLFILLLCLI FLLVLLDY QGMLPVCPLIPGSSTTGTGPCRTCTTPAQGTSMYPSC CCTKPSDGNCTCIPIPSSWAFGKFLWEWASARFSW LSLLVPFVQ WFVGLSPTVWLSVTWMMWYWGPSLYSTLSPFLPLLPIFFCLWVY I (SEQ ID NO:43) (the antigenic loop region, i.e., amino acids 101 - 172, is shown underlined).
• an antibody according to the present disclosure binds to an epitope comprising at least one, at least two, at least three amino acids, or e at least four amino acids of the antigenic loop region of HBsAg, wherein the at least two, at least three, or at least four amino acids are selected from amino acids 115-133 of the S domain of HBsAg, amino acids 120-133 of the S domain of HBsAg, or amino acids 120-130 of the S domain of HBsAg.
• a binding protein (e.g., antibody or an antigen binding fragment thereof) comprises an Fc moiety.
• the Fc moiety may be derived from human origin, e.g., from human IgG1, IgG2, IgG3, and/or IgG4.
• an antibody or antigen binding fragments can comprise an Fc moiety derived from human IgG1.
• an Fc moiety comprises at least one of: a hinge ( e.g ., upper, middle, and/or lower hinge region) domain, a CH2 domain, a CH3 domain, or a variant, portion, or fragment thereof. In some embodiments, an Fc moiety comprises at least a hinge domain, a CH2 domain, or a CH3 domain. In further embodiments, the Fc moiety is a complete Fc moiety.
• the amino acid sequence of an exemplary Fc moiety of human IgG1 isotype is provided in SEQ ID NO:96. The Fc moiety may also comprise one or more amino acid insertions, deletions, or substitutions relative to a naturally occurring Fc moiety.
• an Fc moiety may comprise or consist of: (i) hinge domain (or a portion thereof) fused to a CH2 domain (or a portion thereof), (ii) a hinge domain (or a portion thereof) fused to a CH3 domain (or a portion thereof), (iii) a CH2 domain (or a portion thereof) fused to a CH3 domain (or a portion thereof), (iv) a hinge domain (or a portion thereof), (v) a CH2 domain (or a portion thereof), or (vi) a CH3 domain or a portion thereof.
• An Fc moiety of the present disclosure may be modified such that it varies in amino acid sequence from the complete Fc moiety of a naturally occurring immunoglobulin molecule, while retaining (or enhancing) at least one desirable function conferred by the naturally occurring Fc moiety.
• Such functions include, for example, Fc receptor (FcR) binding, antibody half-life modulation (e.g., by binding to FcRn), ADCC function, protein A binding, protein G binding, and complement binding.
• FcR Fc receptor
• FcyRIII binding reduced binding to FcyRIIIA is found, e.g., for mutation of at least one of E233-G236, P238, D265, N297, A327, P329, D270, Q295, A327, S239, E269, E293, Y296, V303, A327, K338, and D376.
• the Fc moiety of a binding protein of the disclosure can comprise at least a portion known in the art to be required for Protein A binding; and/or the Fc moiety of an antibody of the disclosure comprises at least the portion of an Fc molecule known in the art to be required for protein G binding.
• a retained function comprises the clearance of HBsAg and HBVg.
• an Fc moiety comprises at least a portion known in the art to be required for Fc ⁇ R binding.
• an Fc region or moiety of an Fc polypeptide may comprise a CH2 and/or CH3 domain derived from an immunoglobulin of a first subclass (e.g., an IgG1, IgG2, or IgG4 subclass) and a hinge region from an immunoglobulin of a second subclass (e.g., an IgG3 subclass).
• the Fc region or moiety may comprise a hinge and/or CH2 domain derived from an immunoglobulin of a first subclass (e.g., an IgG4 subclass) and a CH3 domain from an immunoglobulin of a second subclass (e.g ., an IgG1, IgG2, or IgG3 subclass).
• an Fc moiety or Fc region comprises or consists of an amino acid sequence derived from a human immunoglobulin sequence (e.g., from an Fc region or Fc moiety from a human IgG molecule).
• polypeptides may comprise one or more amino acids from another mammalian species.
• a primate Fc moiety or a primate binding site may be included in the subject polypeptides.
• one or more murine amino acids may be present in the Fc moiety or in the Fc region.
• the anti-HBV antibody is HBC34 or an engineered variant thereof, or is HBC24 or an engineered variant thereof.
• HBC34 and HBC24 are human antibodies against HBsAg with high neutralizing activity.
• HBC34 binds to the antigenic loop of HBsAg with high affinity (in the pM range), recognizes all 10 HBV genotypes and 18 mutants, and binds to spherical SVPs with low stoichiometry,
• the activity of HBC34, as measured diagnostically with an immunoassay is 5000 IU/mg.
• the activity of HBIG is ⁇ 1 IU/mg.
• an antibody of the present disclosure is HBC34, or a non-natural variant of an HBC34 antibody.
• non-natural variants of HBC34 include, for example, "HBC34v7,” HBC34v23,” “HBC34v31,” “HBC34v32,” “HBC34v33,” “HBC34v34,” and “HBC34v35.”
• an antibody or antigen-binding fragment of the present disclosure comprises: (i) CDRH1, CDRH2, and CDRH3 amino acid sequences according to SEQ ID NOs:44, 45 or 46, and 47, respectively; and (ii) CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs:48, 49 or 50, and 51 or 52, respectively.
• an antibody or antigen-binding fragment of the present disclosure can comprise any combination of the CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs:44-52.
• an antibody or antigen-binding fragment of the present disclosure comprises: (a) a light chain variable domain (V L ) comprising or consisting of an amino acid sequence that is at least 90%, at least 95%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOs:55-69; and (b) a heavy chain variable domain (Vu) comprising or consisting of an amino acid sequence that is at least 90%, at least 95%, or 100% identical to the amino acid sequence set forth in SEQ ID NO:53 or 54.
• V L light chain variable domain
• Vu heavy chain variable domain
• an antibody or antigen-binding fragment of the present disclosure comprises: (a) a light chain variable domain (V L ) comprising or consisting of an amino acid sequence that is at least 90%, at least 95%, or 100% identical to the amino acid sequence as set forth in any one of SEQ ID NOs:55-57 or 64-69; and (b) a heavy chain variable domain (V H ) comprising or consisting of an amino acid sequence that is at least 90%, at least 95%, or 100% identical to the amino acid sequence set forth in SEQ ID NO:54.
• V L light chain variable domain
• V H heavy chain variable domain
• an antibody or antigen-binding fragment of the present disclosure comprises:
• an antibody or antigen-binding fragment of the present disclosure comprises (a) a light chain comprising or consisting of the amino acid sequence set forth in SEQ ID NO:73, and (b) a heavy chain comprising or consisting of the amino acid sequence set forth in SEQ ID NO:70.
• an antibody or antigen-binding fragment of the present disclosure comprises (a) a light chain comprising or consisting of the amino acid sequence set forth in SEQ ID NO:73, and (b) a heavy chain comprising or consisting of the amino acid sequence set forth in SEQ ID NO:71.
• an antibody or antigen-binding fragment of the present disclosure comprises (a) a light chain comprising or consisting of the amino acid sequence set forth in SEQ ID NO:73, and (b) a heavy chain comprising or consisting of the amino acid sequence set forth in SEQ ID NO:72.
• an antibody or antigen-binding fragment of the present disclosure comprises (a) a light chain comprising or consisting of the amino acid sequence set forth in SEQ ID NO:74, and (b) a heavy chain comprising or consisting of the amino acid sequence set forth in SEQ ID NO:72.
• an antibody or antigen-binding fragment of the present disclosure comprises (a) a light chain comprising or consisting of the amino acid sequence set forth in SEQ ID NO:74, and (b) a heavy chain comprising or consisting of the amino acid sequence set forth in SEQ ID NO:97.
• an antibody or antigen-binding fragment of the present disclosure comprises a CDRH1, a CDRH2, a CDRH3, a CDRL1, a CDRL2, and a CDRL3 having the amino acid sequences according to SEQ ID NOs:77-82, respectively.
• an antibody or antigen-binding fragment of the present disclosure comprises (a) a light chain variable domain (VL) amino acid sequence according to SEQ ID NO:76; and (b) a heavy chain variable domain (V H ) amino acid sequence according to SEQ ID NO:75.
• an antibody or antigen-binding fragment of the present disclosure comprises (a) a light chain variable domain (V L ) that is at least 90%, at least 95%, or 100% identical to the amino acid sequence set forth in SEQ ID NO:76, and (b) a heavy chain variable domain (V H ) that is at least 90%, at least 95%, or 100% identical to the amino acid sequence set forth in SEQ ID NO:75.
• V L light chain variable domain
• V H heavy chain variable domain
• an antibody or antigen binding fragment thereof of the combination therapy is provided as a pharmaceutical composition, which includes the anti-HBV antibody and optionally, a pharmaceutically acceptable carrier.
• a composition may include an anti-HBV antibody, wherein the antibody may make up at least 50% by weight (e.g., 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or more) of the total protein in the composition.
• the antibody may be in purified form.
• compositions of the anti-HBV antibody may include an antimicrobial, particularly if packaged in a multiple dose format. They may comprise detergent, e.g., a Tween (polysorbate), such as Tween 80. When present, detergents are typically present at low levels, e.g., less than 0.01 %. Compositions may also include sodium salts (e.g ., sodium chloride) for tonicity. For example, in some embodiments, a pharmaceutical composition comprises NaCl at a concentration of 10 ⁇ 2mg/ml.
• An antibody composition of the present disclosure may also comprise one or more immunoregulatory agents.
• one or more of the immunoregulatory agents include(s) an adjuvant.
• Methods of preparing a pharmaceutical composition of the anti-HBV antibody may include the steps: (i) preparing the antibody; and (ii) admixing the purified antibody with one or more pharmaceutically acceptable carriers.
• the present disclosure provides methods for treating an HBV infection or a Hepatitis B virus-associated disease.
• the subject has a hepatitis B virus (HBV) infection. In some other embodiments, the subject has both a hepatitis B virus (HBV) infection and a hepatitis D virus (HDV) infection. In some other embodiments, the subject is a human, such as a human being having an HBV infection, especially a chronic hepatitis B virus (CHBV) infection.
• HBV hepatitis B virus
• the terms "treating" or “treatment” refer to a beneficial or desired result including, but not limited to, alleviation or amelioration of one or more signs or symptoms associated with unwanted HBV gene expression or HBV replication, e.g., the presence of serum or liver HBV cccDNA, the presence of serum HBV DNA, the presence of serum or liver HBV antigen, e.g., HBsAg or HBeAg, elevated ALT, elevated AST (normal range is typically considered about 10 to 34 U/L), the absence of or low level of anti-HBV antibodies; a liver injury; cirrhosis; delta hepatitis; acute hepatitis B; acute fulminant hepatitis B; chronic hepatitis B; liver fibrosis; end-stage liver disease; hepatocellular carcinoma; serum sickness-like syndrome; anorexia; nausea; vomiting, low-grade fever; myalgia; fatigability; disordered gustatory acuity and smell sensations (
• liver fibrosis The likelihood of developing, e.g., liver fibrosis, is reduced, for example, when an individual having one or more risk factors for liver fibrosis, e.g., chronic hepatitis B infection, either fails to develop liver fibrosis or develops liver fibrosis with less severity relative to a population having the same risk factors and not receiving treatment as described herein. "Treatment” can also mean prolonging survival as compared to expected survival in the absence of treatment.
• risk factors for liver fibrosis e.g., chronic hepatitis B infection
• prevention refers to the failure to develop a disease, disorder, or condition, or the reduction in the development of a sign or symptom associated with such a disease, disorder, or condition ( e.g ., by a clinically relevant amount), or the exhibition of delayed signs or symptoms delayed ( e.g., by days, weeks, months, or years). Prevention may require the administration of more than one dose.
• treatment of HBV infection results in a "functional cure" of hepatitis B.
• functional cure is understood as clearance of circulating HBsAg and is may be accompanied by conversion to a status in which HBsAg antibodies become detectable using a clinically relevant assay.
• detectable antibodies can include a signal higher than 10 mIU/ml as measured by Chemiluminescent Microparticle Immunoassay (CMIA) or any other immunoassay.
• CMIA Chemiluminescent Microparticle Immunoassay
• Functional cure does not require clearance of all replicative forms of HBV (e.g., cccDNA from the liver). Anti-HBs seroconversion occurs spontaneously in about 0.2-1% of chronically infected patients per year.
• Hepatitis B virus-associated disease is a disease or disorder that is caused by, or associated with HBV infection or replication.
• HBV-associated disease includes a disease, disorder or condition that would benefit from reduction in HBV gene expression or replication.
• HBV-associated diseases include, for example, hepatitis D virus infection, delta hepatitis, acute hepatitis B; acute fulminant hepatitis B; chronic hepatitis B; liver fibrosis; end-stage liver disease; and hepatocellular carcinoma.
• an HBV-associated disease is hepatitis D virus infection.
• Hepatitis D virus or hepatitis delta virus (HDV) is a human pathogen.
• the virus is defective and depends on obligatory helper functions provided by hepatitis B virus (HBV) for transmission; indeed, HDV requires an associated or pre-existing HBV infection to become infectious and thrive, in particular, the viral envelope containing the surface antigen of hepatitis B.
• HBV hepatitis B virus
• HDV can lead to severe acute and chronic forms of liver disease in association with HBV.
• Hepatitis D infection or delta hepatitis is highly endemic to several African countries, the Amazonian region, and the Middle East, while its prevalence is low in industrialized countries, except in the Mediterranean.
• an HBV-associated disease is chronic hepatitis.
• Chronic hepatitis B includes inflammation of the liver that lasts more than six months.
• Subjects having CHB are HBsAg positive and have either high viremia ( ⁇ 10 4 HBV-DNA copies / ml blood) or low viremia ( ⁇ 10 3 HBV-DNA copies / ml blood).
• subjects have been infected with HBV for at least five years.
• subjects have been infected with HBV for at least ten years.
• Subjects having chronic hepatitis B disease can be immune tolerant or have an inactive chronic infection without any evidence of active disease, and they are also asymptomatic. Patients with chronic active hepatitis, especially during the replicative state, may have symptoms similar to those of acute hepatitis. Subjects having chronic hepatitis B disease may have an active chronic infection accompanied by necroinflammatory liver disease, have increased hepatocyte turn-over in the absence of detectable necroinflammation, or have an inactive chronic infection without any evidence of active disease, and they are also asymptomatic. The persistence of HBV infection in CHB subjects is the result of cccHBV DNA. In some embodiments, a subject having CHB is HBeAg positive.
• a subject having CHB is HBeAg negative.
• Subjects having CHB have a level of serum HBV DNA of less than 10 5 and a persistent elevation in transaminases, for examples ALT, AST, and gamma-glutamyl transferase.
• a subject having CHB may have a liver biopsy score of less than 4 ( e.g., a necroinflammatory score).
• an HBV-associated disease is acute fulminant hepatitis B.
• a subject having acute fulminant hepatitis B has symptoms of acute hepatitis and the additional symptoms of confusion or coma (due to the liver's failure to detoxify chemicals) and bruising or bleeding (due to a lack of blood clotting factors).
• liver fibrosis may develop liver fibrosis.
• an HBV-associated disease is liver fibrosis.
• Liver fibrosis, or cirrhosis is defined histologically as a diffuse hepatic process characterized by fibrosis (excess fibrous connective tissue) and the conversion of normal liver architecture into structurally abnormal nodules.
• an HBV-associated disease is end-stage liver disease.
• liver fibrosis may progress to a point where the body may no longer be able to compensate for, e.g., reduced liver function, as a result of liver fibrosis (i.e., decompensated liver), and result in, e.g., mental and neurological symptoms and liver failure.
• An "HDV-associated disorder” or a Hepatitis D-virus-associated disorder” is a disease or disorder associated with expression of an HDV.
• Exemplary HDV-associated disorders include hepatitis B virus infection, acute hepatits B, acute hepatitis D; acute fulminant hepatitis D; chronic hepatitis D; liver fibrosis; end-stage liver disease; and hepatocellular carcinoma.
• Therapeutically effective amount is intended to include the amount of an RNAi agent or anti-HBV antibody, that, when administered to a patient for treating a subject having an HBV infection or HBV-associated disease, is sufficient to effect treatment of the disease (e.g ., by diminishing or maintaining the existing disease or one or more symptoms of disease).
• the "therapeutically effective amount” may vary depending on the RNAi agent and/or anti-HBV antibody, how they are administered, the disease and its severity, and the history, age, weight, family history, genetic makeup, stage of pathological processes mediated by HBV gene expression, the types of preceding or concomitant treatments, if any, and other individual characteristics of the patient to be treated.
• a therapeutically effective amount may require the administration of more than one dose.
• a “therapeutically-effective amount” also includes an amount of an RNAi agent or anti-HBV antibody that produces some desiredeffect at a reasonable benefit/risk ratio applicable to any treatment.
• Therapeutic agents e.g. ,RNAi agents, anti-HBV antibodies
• used in the methods of the present disclosure may be administered in a sufficient amount to produce a reasonable benefit/risk ratio applicable to such treatment.
• sample includes a collection of similar fluids, cells, or tissues isolated from a subject, as well as fluids, cells, or tissues present within a subject.
• biological fluids include blood, serum, and serosal fluids, plasma, lymph, urine, saliva, and the like.
• Tissue samples may include samples from tissues, organs or localized regions.
• samples may be derived from particular organs, parts of organs, or fluids or cells within those organs.
• samples may be derived from the liver (e.g., whole liver or certain segments of liver or certain types of cells in the liver, such as, e.g., hepatocytes).
• a "sample derived from a subject” refers to blood, or plasma or serum obtained from blood drawn from the subject. In further embodiments, a “sample derived from a subject” refers to liver tissue (or subcomponents thereof) or blood tissue (or subcomponents thereof, e.g., serum) derived from the subject.
• Some embodiments of the present disclosure provide methods of treating chronic HBV infection or an HBV-associated disease in a subject in need thereof, comprising: (i) administering to the subject an agent that reduces HBV antigenic load; and (ii) administering to the subject an anti-HBV antibody.
• the agent that reduces HBV antigenic load is administered before the anti-HBV antibody.
• administering the agent that reduces HBV antigenic load before the anti-HBV antibody causes the viral load to be reduced when the anti-HBV antibody is administered.
• the present disclosure provides an agent that reduces HBV antigenic load for use in the treatment of a chronic HBV infection or an HBV-associated disease in a subject, wherein the subject is subsequently administered an anti-HBV antibody.
• the present disclosure provides an anti-HBV antibody for use in the treatment of a chronic HBV infection or an HBV-associated disease in a subject, and the subject has been previously administered an agent that reduces HBV antigenic load.
• expression of at least one HBV gene is reduced after administration of the agent that reduces HBV antigenic load, and the anti-HBV antibody is administered to the subject when expression of the at least one HBV gene is reduced.
• Some embodiments of the present disclosure provide methods of treating chronic HBV infection or an HBV-associated disease in a subject in need thereof, comprising: (i) administering to the subject an inhibitor of HBV gene expression; and (ii) administering to the subject an anti-HBV antibody.
• the inhibitor of HBV gene expression is administered before the anti-HBV antibody.
• administering the inhibitor of HBV gene expression before the anti-HBV antibody causes the viral load to be reduced when the anti-HBV antibody is administered.
• the therapeutically effective amount of the anti-HBV antibody of the combination therapy is less than a therapeutically effective amount of the anti-HBV antibody delivered when the inhibitor of HBV gene expression has not been administered to the subject (e.g ., when the anti-HBV antibody is administered alone as a monotherapy).
• expression of at least one HBV gene is reduced after administering the inhibitor of HBV gene expression, and the anti-HBV antibody is administered to the subject when expression of the at least one HBV gene is reduced.
• the at least one HBV gene is HBV X gene and/or HBsAg.
• the present disclosure provides a method of treating a chronic HBV infection or HBV-associated disease in a subject in need thereof, comprising: administering to the subject an inhibitor of HBV gene expression; and administering to the subject an anti-HBV antibody; and further comprising measuring the amount of HBsAg present in a blood sample from the subject before and after administering the inhibitor of HBV expression, wherein a decrease in HBsAg indicates reduced expression of the at least one HBV gene.
• the present disclosure provides an inhibitor of HBV gene expression for use in the treatment of a chronic HBV infection or an HBV-associated disease in a subject, wherein the subject is subsequently administered an anti-HBV antibody.
• the present disclosure provides an anti-HBV antibody for use in the treatment of a chronic HBV infection or an HBV-associated disease in a subject, and the subject has been previously administered an inhibitor of gene expression.
• expression of at least one HBV gene is reduced after administration of the inhibitor of HBV gene expression, and the anti-HBV antibody is administered to the subject when expression of the at least one HBV gene is reduced.
• the present disclosure provides the use of an inhibitor of HBV gene expression and/or an anti-HBV antibody in the manufacture of a medicament for the treatment of a chronic HBV infection or an HB V-associated disease.
• the inhibitor of HBV gene expression is administered in a single dose, two doses, three doses, four doses, or five doses. In certain particular embodiments, at least the first dose of the inhibitor of HBV gene expression is administered prior to administering the anti-HBV antibody.
• administering the anti-HBV antibody comprises administering the anti-HBV antibody twice per week, once per week, every other week, every two weeks, or once a month.
• administering the anti-HBV antibody comprises administering at least two doses of a therapeutically effective amount of the anti-HBV antibody.
• the at least two doses are administered twice per week, once per week, every other week, every two weeks, or once a month.
• administering the anti-HBV antibody begins at least 1 week after administering the inhibitor of HBV gene expression. In certain embodiments, administering the anti-HBV antibody begins 2 weeks after administering the inhibitor of HBV gene expression. In certain embodiments, administering the anti-HBV antibody begins 8 weeks after administering the inhibitor of HBV gene expression.
• the anti-HBV antibody and the inhibitor of HBV gene expression are each administered subcutaneously.
• compositions for use, or uses in manufacture may recognize HBV genotypes A, B, C, D, E, F, G, H, I, and J.
• the anti-HBV antibody may be a human antibody; a monoclonal antibody; or a bispecific antibody, with a first specificity for HBsAg and a second specificity that stimulates an immune effector (e.g., a second specificity that stimulates cytotoxicity or a vaccinal effect).
• the anti-HBV antibody is a monoclonal antibody.
• the anti-HBV antibody may be HBC34 or a non-natural variant of HBC34 as disclosed herein.
• the anti-HBV antibody comprises CDRs having the amino acid sequences (i) according to SEQ ID NOs:44, 45, 47-49, and 51; or (ii) according to SEQ ID NOs:44, 45, 47-49, and 52.
• the anti-HBV antibody comprises CDRs having the amino acid sequences according to SEQ ID NOs:44, 45, 47, 48, 49, and 51.
• the anti-HBV antibody comprises CDRs having the amino acid sequences according to SEQ ID NOs:44, 45, 47, 48, 49, and 52.
• the anti-HBV antibody comprises: (1) (a) a light chain variable domain (V L ) that is at least 90%, at least 95%, or 100% identical to an amino acid sequence as set forth in any one of SEQ ID NOs:55-63; and (b) a heavy chain variable domain (V H ) that is at least 90%, at least 95%, or 100% identical to an amino acid sequence as set forth in SEQ ID NO:53: or (2) (a) a light chain variable domain (V L ) that is at least 90%, at least 95%, or 100% identical to an amino acid sequence as set forth in any one of SEQ ID NOs:55-57 and 64-69; and (b) a heavy chain variable domain (V H ) that is at least 90%, at least 95%, or 100% identical to an amino acid sequence as set forth in SEQ ID NO:54.
• the anti-HBV antibody comprises: (a) a light chain variable domain (V L ) sequence according to SEQ ID NO:59; and (b) a heavy chain variable domain (V H ) sequence according to SEQ ID NO:53.
• the anti-HBV antibody comprises: (a) a light chain variable domain (V L ) sequence according to SEQ ID NO:58; and (b) a heavy chain variable domain (V H ) sequence according to SEQ ID NO:53.
• the anti-HBV antibody comprises: (a) a light chain that is at least 90%, at least 95%, or 100% identical to an amino acid sequence as set forth in any one of SEQ ID NOs:83-95, and (b) a heavy chain that is at least 90%, at least 95%, or 100% identical to an amino acid sequence as set forth in any one of SEQ ID NOs:70-72, 97 and 98.
• the anti-HBV antibody comprises: (a) a light chain amino acid sequence according to SEQ ID NO:73, and (b) a heavy chain amino acid sequence according to SEQ ID NO:70.
• the anti-HBV antibody comprises: (a) a light chain amino acid sequence according to SEQ ID NO:73, and (b) a heavy chain amino acid sequence according to SEQ ID NO:71.
• the anti-HBV antibody comprises: (a) a light chain amino acid sequence according to SEQ ID NO:74, and (b) a heavy chain amino acid sequence according to SEQ ID NO:70.
• the anti-HBV antibody comprises (a) a light chain variable domain (V L ) that is at least 90%, at least 95%, or 100% identical to an amino acid sequence as set forth in SEQ ID NO:76, and (b) a heavy chain variable domain (V L ) that is at least 90%, at least 95%, or 100% identical to an amino acid sequence as set forth in SEQ ID NO:75.
• a therapeutically effective amount of the anti-HBV antibody is less than a therapeutically effective amount of the anti-HBV antibody delivered when the inhibitor of HBV gene expression has not been administered to the subject.
• the combination therapy may lower the effective dose of the anti-HBV antibody, as compared to administration of the anti-HBV antibody alone.
• compositions for use, or uses in manufacture the the inhibitor is an RNAi agent that inhibits expression of an HBV transcript.
• inhibition of expression of an HBV transcript is measured by rtPCR.
• inhibition of expression of an HBV transcript is measured by a reduction in protein levels as measured by ELISA.
• the RNAi agent is an siRNA having a sense strand comprising 5'-gsusguGfcAfCfUfucgcuucacaL96 -3' (SEQ ID NO:7) and an antisense strand comprising 5'- usGfsuga(Agn)gCfGfaaguGfcAfcacsusu -3' (SEQ ID NO:8)
• an RNAi agent targeting an HBV mRNA is administered to a subject having an HBV infection, and/or an HBV-associated disease, and inhibits HBV gene expression by at least about 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 75%, 75%
• the combination therapy according to the present disclosure comprises administering a nucleot(s)ide analog as a third component.
• nucleot(s)ide analog or “polymerase inhibitor” or “reverse transcriptase inhibitor” is an inhibitor of DNA replication that is structurally similar to a nucleotide or nucleoside and specifically inhibits replication of the HBV cccDNA and does not significantly inhibit the replication of the host ( e.g., human) DNA.
• Such inhibitors include tenofovir disoproxil fumarate (TDF), tenofovir alafenamide (TAF), lamivudine, adefovir dipivoxil, entecavir (ETV), telbivudine, AGX-1009, emtricitabine (FTC), clevudine, ritonavir, dipivoxil, lobucavir, famvir, N-Acetyl-Cysteine (NAC), PC1323, theradigm-HBV, thymosin-alpha, ganciclovir, besifovir (ANA-380/LB-80380), and tenofvir-exaliades (TLX/CMX157).
• TDF tenofovir disoproxil fumarate
• TAF tenofovir alafenamide
• lamivudine lamivudine
• adefovir dipivoxil adefo
• the anti-HBV antibody or the inhibitor of HBV gene expression can be present either in the same pharmaceutical composition as the third active component or, the anti-HBV antibody, the inhibitor of HBV gene expression, and the third active component are present in three different pharmaceutical compositions.
• Such different pharmaceutical compositions may be administered either combined/simultaneously or at separate times or at separate locations ( e.g., separate parts of the body).
• kits including components of the HBV therapy.
• the kit includes one or more anti-HBV antibodies, one or more inhibitors of HBV gene expression, and optionally a third component of HBV combination therapy (e.g., an nucelot(s)ide analog).
• Kits may additionally include instructions for preparing and/or administering the components of the HBV combination therapy.
• AAV/HBV-infected C57BL/6 mice were administered one of fourteen different treatments: (1) an HBV-specific siRNA (HBV02, having an antisense strand of SEQ ID NO:8); (2)-(5) an anti-HBV antibody (a mouse-chimeric version of the HBC34 antibody HBC34v7, HBC34-v7-mu-IgG2a) at one of four doses; (6-7) the HBV02 siRNA and the HBC34-v7-mu-IgG2a antibody, at one of two antibody doses; (8-11) the HBV02 siRNA, the HBC34-v7-mu-IgG2a antibody, and entecavir (ETV), at one of four antibody doses; (12) a control siRNA and a control antibody; (13) entecavir only; or (14) saline only ( see Table 4).
• HBV-specific siRNA HBV02, having an antisense strand of SEQ ID NO:8
• an anti-HBV antibody a mouse-
• HBC34 is a highly neutralizing monoclonal antibody against HBV surface antigen (PreS1, PreS2, and S).
• the HBC34 antibody used in this experiment was a fully murinized HBC34v7, with the exception of the part of the Fab fragment that binds the HBV surface antigen.
• the human HBC34v7 has the V H sequence as set forth in SEQ ID NO:53 and a V L sequence as set forth in SEQ ID NO:56.
• the mouse-chimeric version of HBC34v7 sequences used in the HBC34-v7-mu-IgG2a antibody for this experiment had heavy chain and light chain amino acid sequences as set forth in SEQ ID NOs:99 and 100, respectively.
• siRNA targeting the human transthyretin gene was used as a control siRNA, as it is not expected to cause a descrease in HBV markers of infection in serum.
• control monoclonal antibody (mAb) used in this example was an antibody specific for respiratory syncytial virus, and is not expected to cause a decrease in HBV markers of infection in serum.
• mice C57BL/6 strain
• rAAV8-1.3HBV strain ayw D type: 1.0X10 11 viral genomes per mouse in 200 ⁇ l volume via tail veins injection.
• treatment with test compounds was initiated.
• the dosing schedule is shown in Figure 1 .
• Entecavir was administered orally once per day.
• the HBV-specific siRNA was administered subcutaneously once at the start of the study, and the anti-HBV antibody was administered intraperitoneally twice per week, during weeks three and four of the study.
• a subset of the mice were sacrificed at week four, and the other subset was sacrificed at week six of the study.
• HBeAg serum alanine transferase
• liver HBcAg liver HBsAg
• total HBV DNA in liver by qPCR
• serum anti-HBV antibodies Liver lymphocytes, splenocytes, and lymph nodes (portal/celiac versus inguinal) were assayed to determine the proportion of HBV-specific IFNg - CD4 + cells and IFNg + CD8 - cells.
• HBsAg levels a from mouse serum following treatment with an HBV-specific siRNA, an anti-HBV antibody, and/or entecavir (ETV), or with controls.
• Figures 2B and 3B demonstrate that treatment with both the HBV02 siRNA and the HBC34 antibody (at 15 mg/kg) reduced viral load and HBsAg levels by -3-log 10 , relative to the saline control.
• the reduction of serum HBV DNA and HBsAg were significantly stronger when the HBV02 siRNA and the HBC34 antibody were used in combination relative to treatment with either molecule individually, and the combinatorial effect exceeded the sum of the effects of the monotherapies.
• the combination therapy also reduced viral load and HbsAg levels more than treatment with entecavir alone.
• the effects of the combination of the HBV02 siRNA and the HBC34 antibody were observed regardless of whether entecavir was also administered.
• a combination therapy may allow for effective treatments with: fewer doses of antibody, lower doses of antibody, and/or less invasive administration routes (e.g., subcutaneous instead of intravenous), based at least in part on the reduction of HBsAg load prior to antibody treatment.
• this study demonstrates that administering an siRNA targeting HBV and then administering an antibody targeting HBV effectively decreases serum HBV DNA and HBsAg. Moreover, the individual components appear to interact synergistically, such that the effect of this combination therapy is greater than for each component alone and greater than that which would be expected if the effects were merely additive. Finally, the results suggest that administration of the siRNA reduces serum HBsAg, allowing the antibody to be more effective.
• AAV/HBV-infected C57BL/6 mice were administered one of eleven different treatments: (1) an HBV-specific siRNA (HBV02, having an antisense strand of SEQ ID NO:8; see description in Example 1); (2)-(3) an anti-HBV antibody (a fully murinized HBC24), at one of two doses; (4)-(5) the HBV02 siRNA at one dose, and the fully murinized HBC24 at one of two doses; (6-9) the HBV02 siRNA at one of two doses, and a fully murinized anti-HBV antibody HBC34 (HBC34-v35-mu-IgG2a), at one of three antibody doses; (10) a control siRNA and a control antibody; or (11) PBS only, administered intraperitoneally (see Table 6).
• HBV-specific siRNA HBV02, having an antisense strand of SEQ ID NO:8; see description in Example 1
• an anti-HBV antibody a fully murinized HBC24
• 6 the HBV02
• Treatment HBV02 (mg/kg) HBC24 (mg/kg) HBC34 v35 (mg/kg)
• Control siRNA (mg/kg)
• Control mAb (mg/kg) PBS 1 3 - - - - 2 - 15 - - - 3 - 5 - - - 4 3 15 - - - 5 3 5 - - - 6 3 15 - - - 7 9 15 - - - 8 9 5 - - - 9 9 1 - - - 10 - 3 15 - 11 - - - X
• the HBC24 and HBC34 antibodies used in this experiment are fully murinized with the exception of the part of the Fab fragment that binds the HBV surface antigen.
• the human HBC24 has a V H amino acid sequence as set forth in SEQ ID NO:75 and a V L amino acid sequence as set forth in SEQ ID NO:76.
• the murinized version of HBC24 sequences used in the antibody for this experiment had heavy chain and light chains comprising the amino acid sequences set forth in SEQ ID NOs: 103 and 104, respectively.
• the HBC34 antibody was a murinized HBC34v35 variant, HBC34-v35-mu-IgG2a.
• the human HBC34v35 has a heavy chain amino acid sequence as set forth in SEQ ID NO:70 and a light chain amino acid sequence as set forth in SEQ ID NO:73.
• the murinized version of HBC34v35 sequences used in the HBC34-v35-mu-IgG2a antibody for this experiment had heavy chain and light chains comprising the amino acid sequences set forth in SEQ ID NOs:101 and 102, respectively.
• the control monoclonal antibody was an antibody specific for respiratory syncytial virus, which is not expected to cause a decrease in HBV markers of infection in serum.
• mice C57BL/6 strain
• rAAV8-1.3HBV strain ayw D type
• Each treatment group included five mice.
• the HBV-specific siRNA were administered subcutaneously once at the start of the study, and the anti-HBV antibodies were administered intraperitoneally twice per week, during weeks two and three of the study. The mice were sacrificed at week six of the study.
• An immune-deficient mouse having transplanted human hepatocytes was used to test the effectiveness of a combination therapy with an HBV-specific siRNA and an anti-HBV antibody in clearing HBsAg.
• the PXB-Mouse ® model (PhoenixBio, Japan) uses the uPA/SCID mouse to generate mice with ⁇ 70% repopulation of the mouse liver with human hepatocytes ( Ohshita H and Tateno C, Methods Mol Biol. 1506:91-100, (2017 )).
• cccDNA is established and intrahepatic spread of HBV can occur.
• mice Primary human hepatocytes were transplanted into SCID mice for which mouse hepatocytes had previously been destroyed enzamatically. The mice were T- and B-cell deficient. This model is useful for studying HBV infection including entry, spreading, cccDNA regulation, hepatocyte-intrinsic immune responses, and viral integration into host genome. This model can also be used to study the effect of human IFNa on infection. However, this model does not include the induction of an adaptive immune response. Mice were inoculated via tail vein injection with HBV genotype C at 1.0X10 7 viral genomes per mouse. Treatments began eight weeks post-infection.
• an anti-HBV antibody a fully murinized HBC34v35 antibody, HBC34-v35-mu-IgG2a
• HBV-specific siRNA HBV-specific siRNA
• HBC34v35 The HBC34 antibody used in this experiment, HBC34v35, was fully murinized with the exception of the part of the Fab fragment that binds the HBV surface antigen.
• the human HBC34v35 has a heavy chain amino acid sequence as set forth in SEQ ID NO:70 and a light chain amino acid sequence as set forth in SEQ ID NO:73.
• the murinized version of HBC34v35 sequences used in the HBC34-v35-mu-IgG2a antibody for this experiment had heavy chain and light chains comprising the amino acid sequences set forth in SEQ ID NOs:101 and 102, respectively.
• Serum samples were collected periodically throughout the study, and viral load, HBsAg, and free HBC34 antibody were measured. Measurements were alsotaken for serum HBeAg, serum alanine transferase (ALT), liver HBcAg, liver HBsAg, total HBV DNA in liver (by qPCR), and serum anti-HBV antibodies. Liver lymphocytes, splenocytes, and lymph nodes (portal/celiac versus inguinal) were assayed to determine the proportion of HBV-specific IFNg + CD4 - cells and IFNg - CD8 + cells.
• This study provides experimental support in an authentic infection model that the HBV02 siRNA and an HBC34 antibody, when administered in combination, decrease HBV DNA and HBsAg levels to a greater extent than HBC34 monotherapy.
• a Phase 2 clinical study of an siRNA-antibody combination therapy is conducted to evaluate the efficacy of the combination therapy in human patients with chronic HBV infection.
• Table 8 shows the treatment regimens for the study.
• the study may include additional cohorts to test the effects of additional therapeutics on the combination therapy (e.g., nine cohorts, if two additional therapeutics are tested). Each group/cohort includes fifteen patients. Table 8. Treatment levels and dosages for clinical trial.
• Figure 13 shows a treatment schedule designed for the Phase 2 study.
• the study includes twenty-four weeks of treatment, and twenty-four weeks of follow-up. All patients are non-cirrhotic and NUC suppressed (treated with a nucleot(s)ide analog) upon entering the study. All patient cohorts may receive NUC therapy throughout the study ( e.g ., tenofivir or entecavir administered orally, daily). The study begins with all cohorts receiving an eight-week lead-in treatment with the HBV02 siRNA.
• the doses of HBV02 may be, for example, two doses of 400 mg administered subcutaneously, every four weeks. However, an appropriate dose can be determined by a monotherapy trial prior to the Phase 2 trial.

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